Uses of Class
ubic.gemma.model.expression.experiment.ExpressionExperiment

Packages that use ExpressionExperiment

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.
ubic.gemma.cli.audit
ubic.gemma.cli.util
ubic.gemma.core.analysis.expression
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.qc
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.report
ubic.gemma.core.analysis.service
ubic.gemma.core.analysis.singleCell.aggregate	This package contains classes for subsetting and aggregating single-cell data.
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.datastructure.matrix.io	This package contains I/O utilities for reading and writing expression data matrices.
ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.cellxgene	This package contains classes for loading expression data from CELLxGENE.
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.service
ubic.gemma.core.loader.expression.simple
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.core.tasks.analysis.diffex
ubic.gemma.core.tasks.analysis.expression
ubic.gemma.core.tasks.maintenance
ubic.gemma.core.visualization
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.common.description
ubic.gemma.model.common.quantitationtype
ubic.gemma.model.common.search
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.model.pipeline
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.analysis.expression.pca
ubic.gemma.persistence.service.analysis.expression.sampleCoexpression
ubic.gemma.persistence.service.blacklist	Service for managing blacklisted entities.
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.common.quantitationtype
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.maintenance	Contains classes related to database maintenance.
ubic.gemma.persistence.service.pipeline
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args

Uses of ExpressionExperiment in ubic.gemma.apps

Subclasses with type arguments of type ExpressionExperiment in ubic.gemma.apps

Modifier and Type	Class	Description
class	ExpressionExperimentManipulatingCLI	Base class for CLIs that needs one or more expression experiment as an input.

Methods in ubic.gemma.apps that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
protected Collection<ExpressionExperiment>	ExpressionExperimentManipulatingCLI.preprocessExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)	Preprocess the set of ExpressionExperiment before invoking ExpressionExperimentManipulatingCLI.processExpressionExperiments(Collection) or ExpressionExperimentManipulatingCLI.processExpressionExperiment(ExpressionExperiment).
protected Collection<ExpressionExperiment>	UpdateCellXGeneAccessionsCli.preprocessExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)

Methods in ubic.gemma.apps with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
protected final void	ExpressionExperimentVectorsManipulatingCli.addErrorObject(ExpressionExperiment ee, QuantitationType qt, Exception exception)
protected final void	ExpressionExperimentVectorsManipulatingCli.addErrorObject(ExpressionExperiment ee, QuantitationType qt, String message)
protected final void	ExpressionExperimentVectorsManipulatingCli.addErrorObject(ExpressionExperiment ee, QuantitationType qt, String message, Throwable throwable)
protected final void	ExpressionExperimentVectorsManipulatingCli.addSuccessObject(ExpressionExperiment ee, QuantitationType qt, String message)
protected String	ExpressionExperimentManipulatingCLI.formatExperiment(ExpressionExperiment bas)	Render an experiment to string, with special handling in case of an uninitialized proxy.
protected boolean	ExpressionExperimentManipulatingCLI.noNeedToRun(ExpressionExperiment auditable, Class<? extends AuditEventType> eventClass)
protected void	AffyDataFromCelCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	BatchEffectPopulationCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	DeleteDiffExCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	DeleteExperimentsCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	DifferentialExpressionAnalysisCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	DifferentialExpressionAnalysisWriterCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	ExperimentalDesignImportCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	ExperimentalDesignWriterCLI.processExpressionExperiment(ExpressionExperiment ee)
protected void	ExpressionDataCorrMatCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	ExpressionDataMatrixWriterCLI.processExpressionExperiment(ExpressionExperiment ee)
protected void	ExpressionExperimentDataUpdaterCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	ExpressionExperimentManipulatingCLI.processExpressionExperiment(ExpressionExperiment expressionExperiment)	Process an ExpressionExperiment.
protected void	ExpressionExperimentMetadataChangelogEntryAdderCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	ExpressionExperimentMetadataChangelogViewerCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	ExpressionExperimentMetadataFileAdderCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	ExpressionExperimentPlatformSwitchCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	ExpressionExperimentPrimaryPubCli.processExpressionExperiment(ExpressionExperiment experiment)
protected void	ExpressionExperimentVectorsManipulatingCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	GeeqCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	ListQuantitationTypesCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	LockExpressionDataFileCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	MakeExperimentPrivateCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	MakeExperimentsPublicCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	OrderVectorsByDesignCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	ProcessedDataComputeCLI.processExpressionExperiment(ExpressionExperiment ee)
protected void	ProcessedDataDeleterCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	RawDataDeleterCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	RefreshExperimentCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	ReplaceDataCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	RNASeqDataAddCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	SingleCellCellTypeFactorCreatorCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	SingleCellDataDeleterCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	SingleCellDataLoaderCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	SingleCellSparsityMetricsUpdaterCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	SplitExperimentCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	SVDCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	UpdateCellXGeneAccessionsCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	UpdateEe2AdCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	UpdateEE2CCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	UpdateGeoSourceMetadataCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	VectorMergingCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	VerifyPublicationEvidenceCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	CellLevelMetadataWriterCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)
protected void	DetectQuantitationTypeCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType)
protected void	ExpressionExperimentVectorsManipulatingCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)	Process a set of vectors identified by a QuantitationType.
protected void	ExpressionExperimentVectorsManipulatingCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt, Class<? extends T> vectorType)
protected void	ListQuantitationTypesCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)
protected void	ProcessedDataDeleterCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)
protected void	RawDataDeleterCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)
protected void	RawExpressionDataWriterCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)
protected void	SingleCellDataAggregatorCli.processExpressionExperimentVectors(ExpressionExperiment expressionExperiment, QuantitationType qt)
protected void	SingleCellDataDeleterCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)
protected void	SingleCellDataUpdaterCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)
protected void	SingleCellDataWriterCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)
protected String	ExpressionExperimentManipulatingCLI.readChangelogEntryFromConsole(ExpressionExperiment expressionExperiment, String defaultText)	Read a changelog entry from the console.
protected void	ExpressionExperimentManipulatingCLI.refreshExpressionExperimentFromGemmaWeb(ExpressionExperiment ee, boolean refreshVectors, boolean refreshReports)	Refresh a dataset for Gemma Web.
protected void	ExpressionExperimentManipulatingCLI.refreshExpressionExperimentFromGemmaWebSilently(ExpressionExperiment ee, boolean refreshVectors, boolean refreshReports)	A silent version of ExpressionExperimentManipulatingCLI.refreshExpressionExperimentFromGemmaWeb(ExpressionExperiment, boolean, boolean) that produces a warning via AbstractCLI.addWarningObject(Serializable, String, Throwable) instead of throwing an exception.
protected final Serializable	ExpressionExperimentManipulatingCLI.toBatchObject(ExpressionExperiment object)

Method parameters in ubic.gemma.apps with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
protected void	ExpressionExperimentManipulatingCLI.postprocessExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)	Post-process ExpressionExperiments that were processed by the CLI.
protected void	UpdateEe2AdCli.postprocessExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)
protected void	UpdateEE2CCli.postprocessExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)
protected Collection<ExpressionExperiment>	ExpressionExperimentManipulatingCLI.preprocessExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)	Preprocess the set of ExpressionExperiment before invoking ExpressionExperimentManipulatingCLI.processExpressionExperiments(Collection) or ExpressionExperimentManipulatingCLI.processExpressionExperiment(ExpressionExperiment).
protected Collection<ExpressionExperiment>	UpdateCellXGeneAccessionsCli.preprocessExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)
protected void	ExpressionExperimentManipulatingCLI.processExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)	Process multiple ExpressionExperiment.
protected void	ExpressionExperimentPrimaryPubCli.processExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)
protected void	SingleCellDataLoaderCli.processExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)
protected void	VerifyPublicationEvidenceCli.processExpressionExperiments(Collection<ExpressionExperiment> ees)

Uses of ExpressionExperiment in ubic.gemma.cli.audit

Methods in ubic.gemma.cli.audit with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	CliExpressionExperimentAuditService.computeSampleCorrelation(ExpressionExperiment ee)	Runs the sample-correlation compute step for an experiment.
void	CliExpressionExperimentAuditServiceImpl.computeSampleCorrelation(ExpressionExperiment ee)
void	CliExpressionExperimentAuditService.recordMadePrivate(ExpressionExperiment ee, String note)	Records a MakePrivateEvent on the experiment.
void	CliExpressionExperimentAuditServiceImpl.recordMadePrivate(ExpressionExperiment ee, String note)
void	CliExpressionExperimentAuditService.recordMadePublic(ExpressionExperiment ee, String note)	Records a MakePublicEvent on the experiment.
void	CliExpressionExperimentAuditServiceImpl.recordMadePublic(ExpressionExperiment ee, String note)

Uses of ExpressionExperiment in ubic.gemma.cli.util

Methods in ubic.gemma.cli.util that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	EntityLocator.locateExpressionExperiment(String identifier, boolean useReferencesIfPossible)
ExpressionExperiment	EntityLocatorImpl.locateExpressionExperiment(String identifier, boolean useReferencesIfPossible)	Attempt to locate an experiment using the given identifier.

Methods in ubic.gemma.cli.util with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
BioAssay	EntityLocator.locateBioAssay(ExpressionExperiment ee, String sampleId)
BioAssay	EntityLocator.locateBioAssay(ExpressionExperiment ee, QuantitationType quantitationType, String sampleId)
BioAssay	EntityLocatorImpl.locateBioAssay(ExpressionExperiment ee, String sampleId)
BioAssay	EntityLocatorImpl.locateBioAssay(ExpressionExperiment ee, QuantitationType qt, String sampleId)
CellLevelCharacteristics	EntityLocator.locateCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, String clcIdentifier)
CellLevelCharacteristics	EntityLocatorImpl.locateCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, String clcIdentifier)
CellTypeAssignment	EntityLocator.locateCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String cta)
CellTypeAssignment	EntityLocatorImpl.locateCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String cta)
DifferentialExpressionAnalysis	EntityLocator.locateDiffExAnalysis(ExpressionExperiment ee, String analysisIdentifier)
DifferentialExpressionAnalysis	EntityLocatorImpl.locateDiffExAnalysis(ExpressionExperiment ee, String analysisIdentifier)
ExperimentalFactor	EntityLocator.locateExperimentalFactor(ExpressionExperiment expressionExperiment, String ctfName)
ExperimentalFactor	EntityLocatorImpl.locateExperimentalFactor(ExpressionExperiment expressionExperiment, String identifier)
<T extends DataVector> QuantitationType	EntityLocator.locateQuantitationType(ExpressionExperiment ee, String qt, Class<? extends T> vectorType)
<T extends DataVector> Map.Entry<Class<? extends T>, QuantitationType>	EntityLocator.locateQuantitationType(ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorType)
<T extends DataVector> QuantitationType	EntityLocatorImpl.locateQuantitationType(ExpressionExperiment ee, String qt, Class<? extends T> vectorType)
<T extends DataVector> org.apache.commons.lang3.tuple.Pair<Class<? extends T>, QuantitationType>	EntityLocatorImpl.locateQuantitationType(ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorTypes)

Uses of ExpressionExperiment in ubic.gemma.core.analysis.expression

Methods in ubic.gemma.core.analysis.expression with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
boolean	AnalysisUtilService.deleteOldAnalyses(ExpressionExperiment expExp)	Remove all analyses for the experiment (Differential, Coexpression and PCA).
boolean	AnalysisUtilServiceImpl.deleteOldAnalyses(ExpressionExperiment expExp)

Uses of ExpressionExperiment in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
int	DifferentialExpressionAnalyzerService.deleteAnalyses(ExpressionExperiment expressionExperiment)	Delete any differential expression analyses associated with the experiment.
int	DifferentialExpressionAnalyzerService.deleteAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> analysesToDelete)	Delete the specified differential expression analyses associated with the experiment.
int	DifferentialExpressionAnalyzerServiceImpl.deleteAnalyses(ExpressionExperiment expressionExperiment)
int	DifferentialExpressionAnalyzerServiceImpl.deleteAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> analysesToDelete)
void	DifferentialExpressionAnalyzerService.deleteAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis existingAnalysis)	Deletes the given analysis.
void	DifferentialExpressionAnalyzerServiceImpl.deleteAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis existingAnalysis)	SUPPORTS overrides the class-level NEVER so a caller that is already in a transaction -- ExpressionExperimentService.applyDesignChange(ExpressionExperiment, ExperimentalDesignValueObject) cascading invalidated analyses -- can route through here instead of calling differentialExpressionAnalysisService.remove, which is database-only and leaves the archive and result-set TSV caches on the deployment volume.
void	DifferentialExpressionAnalyzerServiceImpl.deleteStatistics(ExpressionExperiment ee, DifferentialExpressionAnalysis analysis)	Remove old files which will otherwise be cruft.
Collection<ExpressionAnalysisResultSet>	DifferentialExpressionAnalyzerService.extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate, DifferentialExpressionAnalysisConfig config)	Like redo, but we don't save the results, we just add the full set of results to the analysis given.
Collection<ExpressionAnalysisResultSet>	DifferentialExpressionAnalyzerServiceImpl.extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate, DifferentialExpressionAnalysisConfig baseConfig)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.getAnalyses(ExpressionExperiment expressionExperiment)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.getAnalyses(ExpressionExperiment expressionExperiment)
DifferentialExpressionAnalysis	DifferentialExpressionAnalyzerService.persistAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)	Made public for testing purposes only.
DifferentialExpressionAnalysis	DifferentialExpressionAnalyzerServiceImpl.persistAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)	Made public for testing purposes only.
void	DifferentialExpressionAnalyzerAuditService.recordAnalysisPersisted(ExpressionExperiment ee, String note, DifferentialExpressionAnalysisPayload payload)	Emit a DifferentialExpressionAnalysisEvent for ee with the given payload.
void	DifferentialExpressionAnalyzerAuditServiceImpl.recordAnalysisPersisted(ExpressionExperiment ee, String note, DifferentialExpressionAnalysisPayload payload)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> deas, DifferentialExpressionAnalysisConfig config, boolean ignoreFailingAnalyses)	Redo multiple analyses.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> deas, DifferentialExpressionAnalysisConfig config, boolean ignoreFailingAnalyses)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea)	Redo an analysis.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea, DifferentialExpressionAnalysisConfig config)	Redo an analysis.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	DiffExAnalyzer.run(ExpressionExperiment expressionExperiment, Map<FactorValue, ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset with a pre-existing subset structure.
Collection<DifferentialExpressionAnalysis>	DiffExAnalyzer.run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset.
Collection<DifferentialExpressionAnalysis>	LinearModelAnalyzer.run(ExpressionExperiment ee, Map<FactorValue, ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	LinearModelAnalyzer.run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	I apologize for this being so complicated.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)

Uses of ExpressionExperiment in ubic.gemma.core.analysis.preprocess

Methods in ubic.gemma.core.analysis.preprocess with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
Integer	PreprocessorHelperService.batchCorrect(ExpressionExperiment ee)	If possible, batch-correct the processed data vectors via ComBat.
Integer	PreprocessorHelperServiceImpl.batchCorrect(ExpressionExperiment ee)	If possible, batch correct the processed data vectors.
Collection<RawExpressionDataVector>	TwoChannelMissingValues.computeMissingValues(ExpressionExperiment ee)	Deprecated.
Collection<RawExpressionDataVector>	TwoChannelMissingValues.computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)	Deprecated.
Collection<RawExpressionDataVector>	TwoChannelMissingValuesImpl.computeMissingValues(ExpressionExperiment ee)	Deprecated.
Collection<RawExpressionDataVector>	TwoChannelMissingValuesImpl.computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)	Deprecated.
MeanVarianceRelation	MeanVarianceService.create(ExpressionExperiment ee, boolean forceRecompute)	Retrieve (and if necessary compute) the mean-variance relationship for the experiment
MeanVarianceRelation	MeanVarianceServiceImpl.create(ExpressionExperiment ee, boolean forceRecompute)
void	MeanVarianceServiceHelper.createMeanVariance(ExpressionExperiment ee, MeanVarianceRelation mvr)
ExpressionDataDoubleMatrix	MeanVarianceServiceHelper.getIntensities(ExpressionExperiment ee)
Optional<Collection<OutlierDetails>>	OutlierDetectionService.getOutlierDetails(ExpressionExperiment ee)	Obtain existing outlier details from a previous OutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment) invocation.
Optional<Collection<OutlierDetails>>	OutlierDetectionServiceImpl.getOutlierDetails(ExpressionExperiment ee)
Collection<OutlierDetails>	OutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment ee)	Identify outliers by median correlation for the given dataset.
Collection<OutlierDetails>	OutlierDetectionServiceImpl.identifyOutliersByMedianCorrelation(ExpressionExperiment ee)
int	VectorMergingService.mergeVectors(ExpressionExperiment expExp)	Merge the raw data vectors of a given experiment.
int	VectorMergingServiceImpl.mergeVectors(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	TwoChannelMissingValueHelperService.persist(ExpressionExperiment source, Collection<RawExpressionDataVector> results)	Deprecated.
default void	PreprocessorService.process(ExpressionExperiment ee)	Preprocess a dataset.
default void	PreprocessorService.process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)	Preprocess a dataset.
void	PreprocessorService.process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch, boolean ignoreDiagnosticFailure)	Preprocess a dataset.
void	PreprocessorServiceImpl.process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch, boolean ignoreDiagnosticsFailure)
void	PreprocessorService.processDiagnostics(ExpressionExperiment ee)	Create or update the sample correlation, PCA and M-V data.
void	PreprocessorServiceImpl.processDiagnostics(ExpressionExperiment ee)
void	PreprocessorHelperService.processForMeanVarianceRelation(ExpressionExperiment ee)	Compute and persist the mean-variance scatter used for the heteroscedasticity diagnostic plot.
void	PreprocessorHelperServiceImpl.processForMeanVarianceRelation(ExpressionExperiment ee)	Create the scatter plot to evaluate heteroscedasticity.
void	PreprocessorHelperService.processForPca(ExpressionExperiment ee)	Run SVD / PCA for diagnostics.
void	PreprocessorHelperServiceImpl.processForPca(ExpressionExperiment ee)
void	PreprocessorHelperService.processForSampleCorrelation(ExpressionExperiment ee)	Compute and persist the sample-sample correlation matrix used for the diagnostic heatmap.
void	PreprocessorHelperServiceImpl.processForSampleCorrelation(ExpressionExperiment ee)	Create the heatmaps used to judge similarity among samples.
ExpressionExperimentSet	SplitExperimentService.split(ExpressionExperiment expressionExperiment, ExperimentalFactor splitOn, boolean postProcess)	Split an experiment into multiple experiments based on a factor.
ExpressionExperimentSet	SplitExperimentServiceImpl.split(ExpressionExperiment toSplit, ExperimentalFactor splitOn, boolean postProcess)

Constructors in ubic.gemma.core.analysis.preprocess with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	FilteringRelatedPreprocessingException(ExpressionExperiment ee, FilteringException cause)
	PreprocessingException(ExpressionExperiment ee, String message)
	PreprocessingException(ExpressionExperiment ee, String message, Throwable cause)
	PreprocessingException(ExpressionExperiment ee, Throwable cause)
	QuantitationTypeConversionRelatedPreprocessingException(ExpressionExperiment ee, QuantitationTypeConversionException cause)
	QuantitationTypeDetectionRelatedPreprocessingException(ExpressionExperiment ee, QuantitationTypeDetectionException cause)
	SampleCoexpressionRelatedPreprocessingException(ExpressionExperiment ee, Throwable cause)
	SVDRelatedPreprocessingException(ExpressionExperiment ee, SVDException cause)

Uses of ExpressionExperiment in ubic.gemma.core.analysis.preprocess.batcheffects

Methods in ubic.gemma.core.analysis.preprocess.batcheffects that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Map<ExpressionExperiment, Boolean>	ExpressionExperimentBatchInformationService.checkHasBatchInfo(Collection<ExpressionExperiment> ees)	Batch counterpart to ExpressionExperimentBatchInformationService.checkHasBatchInfo(ExpressionExperiment).
Map<ExpressionExperiment, Boolean>	ExpressionExperimentBatchInformationServiceImpl.checkHasBatchInfo(Collection<ExpressionExperiment> ees)

Methods in ubic.gemma.core.analysis.preprocess.batcheffects with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
boolean	ExpressionExperimentBatchCorrectionService.checkCorrectability(ExpressionExperiment ee)	Check if the given experiment is correctable for batch effects.
boolean	ExpressionExperimentBatchCorrectionServiceImpl.checkCorrectability(ExpressionExperiment ee)
boolean	ExpressionExperimentBatchInformationService.checkHasBatchInfo(ExpressionExperiment ee)	Check if the given experiment has batch information.
boolean	ExpressionExperimentBatchInformationServiceImpl.checkHasBatchInfo(ExpressionExperiment ee)
boolean	ExpressionExperimentBatchInformationService.checkHasUsableBatchInfo(ExpressionExperiment ee)	Check if the given experiment has usable batch information.
boolean	ExpressionExperimentBatchInformationServiceImpl.checkHasUsableBatchInfo(ExpressionExperiment ee)
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionService.comBat(ExpressionExperiment ee)	Run ComBat using default settings (parametric)
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionService.comBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix mat)	Run ComBat with a specific data matrix.
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionServiceImpl.comBat(ExpressionExperiment ee)
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionServiceImpl.comBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix originalDataMatrix)
ExperimentalFactor	BatchInfoPopulationHelperService.createBatchFactor(ExpressionExperiment ee, Map<BioMaterial, Date> dates)
ExperimentalFactor	BatchInfoPopulationHelperServiceImpl.createBatchFactor(ExpressionExperiment ee, Map<BioMaterial, Date> dates)
ExperimentalFactor	BatchInfoPopulationHelperService.createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial, String> headers)	For RNA-seq, we based the batching on the available device/run/flowcell/lane information
ExperimentalFactor	BatchInfoPopulationHelperServiceImpl.createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial, String> headers)	For RNA-seq, we based the batching on the available device/run/flowcell/lane information
void	BatchInfoPopulationService.fillBatchInformation(ExpressionExperiment ee, boolean force)	Attempt to obtain batch information from the data provider and populate it into the given experiment.
void	BatchInfoPopulationServiceImpl.fillBatchInformation(ExpressionExperiment ee, boolean force)
static Map<String,BioAssay>	BatchInfoParser.getAccessionToBioAssayMap(ExpressionExperiment ee)
String	ExpressionExperimentBatchInformationService.getBatchConfoundAsHtmlString(ExpressionExperiment ee)	Summarize the batch confounds for a given dataset or its subsets in an HTML string.
String	ExpressionExperimentBatchInformationServiceImpl.getBatchConfoundAsHtmlString(ExpressionExperiment ee)
BatchEffectDetails	ExpressionExperimentBatchInformationService.getBatchEffectDetails(ExpressionExperiment ee)	Obtain the full batch effect details of a given experiment.
BatchEffectDetails	ExpressionExperimentBatchInformationServiceImpl.getBatchEffectDetails(ExpressionExperiment ee)
Map<BioMaterial, Date>	BatchInfoParser.getBatchInfo(ExpressionExperiment ee, Collection<File> files)
List<BatchConfound>	ExpressionExperimentBatchInformationService.getSignificantBatchConfounds(ExpressionExperiment ee)	Obtain the significant batch confounds for a dataset.
List<BatchConfound>	ExpressionExperimentBatchInformationServiceImpl.getSignificantBatchConfounds(ExpressionExperiment ee)
Map<ExpressionExperimentSubSet, List<BatchConfound>>	ExpressionExperimentBatchInformationService.getSignificantBatchConfoundsForSubsets(ExpressionExperiment ee)	Obtain the significant batch confounds for a dataset subsets.
Map<ExpressionExperimentSubSet, List<BatchConfound>>	ExpressionExperimentBatchInformationServiceImpl.getSignificantBatchConfoundsForSubsets(ExpressionExperiment ee)
boolean	ExpressionExperimentBatchInformationService.hasSignificantBatchConfound(ExpressionExperiment ee)	Check if a given experiment has a significant batch confound.
boolean	ExpressionExperimentBatchInformationServiceImpl.hasSignificantBatchConfound(ExpressionExperiment ee)
void	BatchInfoPopulationHelperService.recordBatchInformationFetched(ExpressionExperiment ee, String note)	Record a BatchInformationFetchingEvent on ee.
void	BatchInfoPopulationHelperServiceImpl.recordBatchInformationFetched(ExpressionExperiment ee, String note)	Record a BatchInformationFetchingEvent on ee.
void	BatchInfoPopulationHelperService.recordSingleBatchDetermination(ExpressionExperiment ee, String note)	Record a SingleBatchDeterminationEvent on ee.
void	BatchInfoPopulationHelperServiceImpl.recordSingleBatchDetermination(ExpressionExperiment ee, String note)	Record a SingleBatchDeterminationEvent on ee.

Method parameters in ubic.gemma.core.analysis.preprocess.batcheffects with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Map<ExpressionExperiment, Boolean>	ExpressionExperimentBatchInformationService.checkHasBatchInfo(Collection<ExpressionExperiment> ees)	Batch counterpart to ExpressionExperimentBatchInformationService.checkHasBatchInfo(ExpressionExperiment).
Map<ExpressionExperiment, Boolean>	ExpressionExperimentBatchInformationServiceImpl.checkHasBatchInfo(Collection<ExpressionExperiment> ees)

Constructors in ubic.gemma.core.analysis.preprocess.batcheffects with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	BatchInfoMissingException(ExpressionExperiment ee, String message)
	BatchInfoMissingException(ExpressionExperiment ee, String message, Throwable cause)
	BatchInfoPopulationException(ExpressionExperiment ee, String message)
	BatchInfoPopulationException(ExpressionExperiment ee, String message, Throwable cause)
	BatchInfoPopulationException(ExpressionExperiment ee, Throwable cause)
	FASTQHeadersPresentButNotUsableException(ExpressionExperiment ee, String message)
	SingletonBatchesException(ExpressionExperiment ee, String message)
	UnsupportedRawdataFileFormatException(ExpressionExperiment ee, String message)

Uses of ExpressionExperiment in ubic.gemma.core.analysis.preprocess.qc

Methods in ubic.gemma.core.analysis.preprocess.qc with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
Optional<SequencingQcMetrics>	SequencingQcMetricsService.getSequencingQcMetrics(ExpressionExperiment ee)	Obtain the sequencing QC metrics for an experiment.
Optional<SequencingQcMetrics>	SequencingQcMetricsServiceImpl.getSequencingQcMetrics(ExpressionExperiment ee)

Uses of ExpressionExperiment in ubic.gemma.core.analysis.preprocess.svd

Methods in ubic.gemma.core.analysis.preprocess.svd that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	SVDResult.getExperimentAnalyzed()	Experiment or subset this is for.

Methods in ubic.gemma.core.analysis.preprocess.svd with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
Set<ExperimentalFactor>	SVDService.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
Set<ExperimentalFactor>	SVDServiceImpl.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
SVDResult	SVDService.getSvd(ExpressionExperiment ee)	Obtain the SVD analysis for the given experiment, if it exists.
SVDResult	SVDServiceImpl.getSvd(ExpressionExperiment ee)	Get the SVD information for experiment with id given.
SVDResult	SVDService.getSvdFactorAnalysis(ExpressionExperiment ee)	Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
SVDResult	SVDServiceImpl.getSvdFactorAnalysis(ExpressionExperiment ee)
Map<ProbeLoading, DoubleVectorValueObject>	SVDService.getTopLoadedVectors(ExpressionExperiment ee, int component, int count)
Map<ProbeLoading, DoubleVectorValueObject>	SVDServiceImpl.getTopLoadedVectors(ExpressionExperiment ee, int component, int count)
boolean	SVDService.hasSvd(ExpressionExperiment ee)	Check if a dataset has a SVD analysis.
boolean	SVDServiceImpl.hasSvd(ExpressionExperiment ee)
SVDResult	SVDService.svd(ExpressionExperiment ee)	Compute and update the SVD analysis fo the given experiment.
SVDResult	SVDServiceImpl.svd(ExpressionExperiment ee)

Uses of ExpressionExperiment in ubic.gemma.core.analysis.report

Methods in ubic.gemma.core.analysis.report that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	WhatsNew.getNewExpressionExperiments()
Collection<ExpressionExperiment>	WhatsNew.getUpdatedExpressionExperiments()

Methods in ubic.gemma.core.analysis.report with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
String	ExpressionExperimentReportService.recalculateExperimentBatchConfound(ExpressionExperiment ee)	Recompute the batch confound for ee and persist it; emit a BatchProblemsUpdateEvent only when the value actually changed.
String	ExpressionExperimentReportServiceImpl.recalculateExperimentBatchConfound(ExpressionExperiment ee)
String	ExpressionExperimentReportService.recalculateExperimentBatchEffect(ExpressionExperiment ee)	Recompute the batch effect for ee and persist it; emit a BatchProblemsUpdateEvent only when the effect or its statistics actually changed.
String	ExpressionExperimentReportServiceImpl.recalculateExperimentBatchEffect(ExpressionExperiment ee)
void	ExpressionExperimentReportService.recalculateExperimentBatchInfo(ExpressionExperiment ee)	Recalculates the batch effect and batch confound information for the given dataset.
void	ExpressionExperimentReportServiceImpl.recalculateExperimentBatchInfo(ExpressionExperiment ee)
void	ExpressionExperimentReportService.recalculateExperimentBatchInfoAsAdmin(ExpressionExperiment ee)	Recalculates the batch effect and batch confound information for the given dataset.
void	ExpressionExperimentReportServiceImpl.recalculateExperimentBatchInfoAsAdmin(ExpressionExperiment ee)

Uses of ExpressionExperiment in ubic.gemma.core.analysis.service

Methods in ubic.gemma.core.analysis.service that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
DoubleMatrix<Gene, ExpressionExperiment>	ExpressionDataMatrixService.getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
DoubleMatrix<Gene, ExpressionExperiment>	ExpressionDataMatrixServiceImpl.getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)

Methods in ubic.gemma.core.analysis.service with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	ExpressionMetadataChangelogFileService.addChangelogEntry(ExpressionExperiment expressionExperiment, String changelogEntry)
void	ExpressionMetadataChangelogFileService.addChangelogEntry(ExpressionExperiment expressionExperiment, String changelogEntry, LocalDate date)	Add a changelog entry to the changelog file of the given experiment.
void	ExpressionMetadataChangelogFileServiceImpl.addChangelogEntry(ExpressionExperiment expressionExperiment, String changelogEntry)
void	ExpressionMetadataChangelogFileServiceImpl.addChangelogEntry(ExpressionExperiment expressionExperiment, String changelogEntry, LocalDate date)
Path	ExpressionDataFileService.copyMetadataFile(ExpressionExperiment ee, Path existingFile, String filename, boolean forceWrite)	Copy a generic metadata file.
Path	ExpressionDataFileService.copyMetadataFile(ExpressionExperiment ee, Path existingFile, ExpressionExperimentMetaFileType type, boolean forceWrite)	Copy a metadata file to the location of a given metadata type.
Path	ExpressionDataFileServiceImpl.copyMetadataFile(ExpressionExperiment ee, Path existingFile, String filename, boolean forceWrite)
Path	ExpressionDataFileServiceImpl.copyMetadataFile(ExpressionExperiment ee, Path existingFile, ExpressionExperimentMetaFileType type, boolean forceWrite)
Path	ExpressionDataFileService.copyMultiQCReport(ExpressionExperiment ee, Path existingFile, ExpressionExperimentMetaFileType type, boolean forceWrite)	Copy a MultiQC report.
Path	ExpressionDataFileServiceImpl.copyMultiQCReport(ExpressionExperiment ee, Path existingFile, ExpressionExperimentMetaFileType fileType, boolean forceWrite)
int	ExpressionDataFileService.deleteAllAnalysisFiles(ExpressionExperiment ee)	Delete all analyses files for a given experiment.
int	ExpressionDataFileServiceImpl.deleteAllAnalysisFiles(ExpressionExperiment ee)
int	ExpressionDataFileService.deleteAllAnnotatedFiles(ExpressionExperiment ee)	Delete all files that contain platform annotations for a given experiment.
int	ExpressionDataFileServiceImpl.deleteAllAnnotatedFiles(ExpressionExperiment ee)
int	ExpressionDataFileService.deleteAllDataFiles(ExpressionExperiment ee, QuantitationType qt)	Delete all data files for a given QT.
int	ExpressionDataFileServiceImpl.deleteAllDataFiles(ExpressionExperiment ee, QuantitationType qt)
int	ExpressionDataFileService.deleteAllFiles(ExpressionExperiment ee)	Delete any existing design, coexpression, data, or differential expression data files.
int	ExpressionDataFileServiceImpl.deleteAllFiles(ExpressionExperiment ee)
int	ExpressionDataFileService.deleteAllProcessedDataFiles(ExpressionExperiment ee)	Delete all the processed files for a given experiment.
int	ExpressionDataFileServiceImpl.deleteAllProcessedDataFiles(ExpressionExperiment ee)
boolean	ExpressionDataFileService.deleteCoexpressionDataFile(ExpressionExperiment ee)	Delete a coexpression data file if it exists.
boolean	ExpressionDataFileServiceImpl.deleteCoexpressionDataFile(ExpressionExperiment ee)
boolean	ExpressionDataFileService.deleteDataFile(ExpressionExperiment ee, boolean filtered, ExpressionExperimentDataFileType type)	Delete a processed data file if it exists.
boolean	ExpressionDataFileService.deleteDataFile(ExpressionExperiment ee, QuantitationType qt, ExpressionExperimentDataFileType type)	Delete a raw or single-cell data file if it exists.
boolean	ExpressionDataFileServiceImpl.deleteDataFile(ExpressionExperiment ee, boolean filtered, ExpressionExperimentDataFileType type)
boolean	ExpressionDataFileServiceImpl.deleteDataFile(ExpressionExperiment ee, QuantitationType qt, ExpressionExperimentDataFileType type)
boolean	ExpressionDataFileService.deleteDesignFile(ExpressionExperiment ee)	Delete the experimental design file for a given experiment.
boolean	ExpressionDataFileServiceImpl.deleteDesignFile(ExpressionExperiment ee)
boolean	ExpressionDataFileService.deleteMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type)	Delete a metadata file.
boolean	ExpressionDataFileServiceImpl.deleteMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type)
void	ExpressionDataDeleterService.deleteProcessedData(ExpressionExperiment ee)
void	ExpressionDataDeleterServiceImpl.deleteProcessedData(ExpressionExperiment ee)
boolean	ExpressionDataFileService.deleteProcessedDataDesignFile(ExpressionExperiment ee)
boolean	ExpressionDataFileServiceImpl.deleteProcessedDataDesignFile(ExpressionExperiment ee)
void	ExpressionDataDeleterService.deleteRawData(ExpressionExperiment ee, QuantitationType qt)	Delete raw data vectors and associated data files.
void	ExpressionDataDeleterServiceImpl.deleteRawData(ExpressionExperiment ee, QuantitationType qt)
void	ExpressionDataDeleterService.deleteSingleCellData(ExpressionExperiment ee, QuantitationType qt)
void	ExpressionDataDeleterServiceImpl.deleteSingleCellData(ExpressionExperiment ee, QuantitationType qt)
Path	ExpressionMetadataChangelogFileService.getChangelogFilePath(ExpressionExperiment expressionExperiment)	Absolute path of the changelog file for expressionExperiment, whether or not it exists yet.
Path	ExpressionMetadataChangelogFileServiceImpl.getChangelogFilePath(ExpressionExperiment expressionExperiment)
static String	ExpressionDataFileUtils.getCoexpressionDataFilename(ExpressionExperiment ee)	Obtain the filename for writing coexpression data.
LockedPath	ExpressionDataFileService.getDataFile(ExpressionExperiment ee, QuantitationType qt, ExpressionExperimentDataFileType type, boolean exclusive, long timeout, TimeUnit timeUnit)
LockedPath	ExpressionDataFileServiceImpl.getDataFile(ExpressionExperiment ee, QuantitationType qt, ExpressionExperimentDataFileType type, boolean exclusive, long timeout, TimeUnit timeUnit)
static String	ExpressionDataFileUtils.getDataOutputFilename(ExpressionExperiment ee, boolean filtered, String suffix)	Obtain a filename for writing the processed data.
static String	ExpressionDataFileUtils.getDataOutputFilename(ExpressionExperiment ee, List<BioAssay> assays, boolean filtered, String suffix)
static String	ExpressionDataFileUtils.getDataOutputFilename(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType type, String suffix)	Obtain the filename for writing a specific QT.
static String	ExpressionDataFileUtils.getDataOutputFilename(ExpressionExperiment ee, QuantitationType type, String suffix)	Obtain the filename for writing a specific QT.
static String	ExpressionDataFileUtils.getDesignFileName(ExpressionExperiment ee, boolean useProcessedData)	Obtain the filename for writing experimental design.
static String	ExpressionDataFileUtils.getDesignFileName(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain the filename for writing experimental design for a specific QT.
static String	ExpressionDataFileUtils.getEigenGenesFilename(ExpressionExperiment ee)
static String	ExpressionDataFileUtils.getExpressionExperimentMetadataDirname(ExpressionExperiment ee)	Forms a folder name where the given experiments metadata will be located (within the ${gemma.appdata.home}/metadata directory).
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform, ExpressionExperimentFilterResult result)	Provide a filtered expression data matrix, reporting the per-stage attrition into a caller-supplied result.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, ExpressionExperimentFilterConfig filterConfig)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform, ExpressionExperimentFilterResult result)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, ExpressionExperimentFilterConfig filterConfig)
static String	ExpressionDataFileUtils.getMeanVarianceRelationFilename(ExpressionExperiment ee)
LockedPath	ExpressionDataFileService.getMetadataFile(ExpressionExperiment ee, String filename, boolean exclusive)
LockedPath	ExpressionDataFileService.getMetadataFile(ExpressionExperiment ee, String filename, boolean exclusive, long timeout, TimeUnit timeUnit)
Optional<LockedPath>	ExpressionDataFileService.getMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type, boolean exclusive)	Locate a metadata file.
LockedPath	ExpressionDataFileServiceImpl.getMetadataFile(ExpressionExperiment ee, String filename, boolean exclusive)
LockedPath	ExpressionDataFileServiceImpl.getMetadataFile(ExpressionExperiment ee, String filename, boolean exclusive, long timeout, TimeUnit timeUnit)
Optional<LockedPath>	ExpressionDataFileServiceImpl.getMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type, boolean exclusive)
static String	ExpressionDataFileUtils.getMetadataOutputFilename(ExpressionExperiment ee, QuantitationType qt, String suffix)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getProcessedExpressionDataMatrix(ExpressionExperiment ee)	Obtain the processed expression data matrix for a given experiment.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getProcessedExpressionDataMatrix(ExpressionExperiment ee, boolean thawAssays)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getProcessedExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getProcessedExpressionDataMatrix(ExpressionExperiment ee)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getProcessedExpressionDataMatrix(ExpressionExperiment ee, boolean thawAssays)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getProcessedExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getRawExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain a raw expression data matrix for a given quantitation type
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getRawExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)
String	ExpressionMetadataChangelogFileService.readChangelog(ExpressionExperiment expressionExperiment)	Read the content of the changelog file of the given experiment.
String	ExpressionMetadataChangelogFileServiceImpl.readChangelog(ExpressionExperiment expressionExperiment)
void	BioAssayMetadataAuditService.recordSampleMetadataChange(ExpressionExperiment ee, String note, SampleMetadataPayload payload)
void	BioAssayMetadataAuditServiceImpl.recordSampleMetadataChange(ExpressionExperiment ee, String note, SampleMetadataPayload payload)
void	OutlierFlaggingAuditService.recordSampleRemoval(ExpressionExperiment ee, String note, SampleRemovalPayload payload)	Emit a SampleRemovalEvent for ee with the given payload.
void	OutlierFlaggingAuditServiceImpl.recordSampleRemoval(ExpressionExperiment ee, String note, SampleRemovalPayload payload)
void	OutlierFlaggingAuditService.recordSampleRemovalReversion(ExpressionExperiment ee, String note, SampleRemovalPayload payload)	Emit a SampleRemovalReversionEvent for ee with the given payload.
void	OutlierFlaggingAuditServiceImpl.recordSampleRemovalReversion(ExpressionExperiment ee, String note, SampleRemovalPayload payload)
Collection<BioAssay>	BioAssayMetadataService.setExtractedMolecule(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)	Set extractedMolecule on the given samples.
Collection<BioAssay>	BioAssayMetadataServiceImpl.setExtractedMolecule(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)
Collection<BioAssay>	BioAssayMetadataService.setLibrarySelection(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)	Set librarySelection on the given samples.
Collection<BioAssay>	BioAssayMetadataServiceImpl.setLibrarySelection(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)
Collection<BioAssay>	BioAssayMetadataService.setLibraryStrategy(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)	Set libraryStrategy on the given samples.
Collection<BioAssay>	BioAssayMetadataServiceImpl.setLibraryStrategy(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)
void	ExpressionDataFileService.streamAndWriteProcessedExpressionData(ExpressionExperiment ee, boolean filtered, boolean forceWrite, Writer writer, boolean autoFlush)	Stream the processed expression data to the writer while populating the cache file in the same pass.
void	ExpressionDataFileServiceImpl.streamAndWriteProcessedExpressionData(ExpressionExperiment ee, boolean filtered, boolean forceWrite, Writer writer, boolean autoFlush)
void	ExpressionDataFileService.streamAndWriteRawExpressionData(ExpressionExperiment ee, QuantitationType qt, boolean forceWrite, Writer writer, boolean autoFlush)	Raw sibling of ExpressionDataFileService.streamAndWriteProcessedExpressionData(ExpressionExperiment, boolean, boolean, Writer, boolean).
void	ExpressionDataFileServiceImpl.streamAndWriteRawExpressionData(ExpressionExperiment ee, QuantitationType qt, boolean forceWrite, Writer writer, boolean autoFlush)
void	ExpressionDataFileService.streamAndWriteTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Writer writer, boolean autoFlush)	Tabular single-cell sibling of ExpressionDataFileService.streamAndWriteProcessedExpressionData(ExpressionExperiment, boolean, boolean, Writer, boolean) — the payloads here are the largest in the system, so the duplicated cold build this replaces was at its most expensive on this path: two concurrent full scans of the single-cell vectors per cold request.
void	ExpressionDataFileServiceImpl.streamAndWriteTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeCellBrowserSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useBioAssayIds, boolean useRawColumnNames, int fetchSize, boolean useCursorFetchIfSupported, Writer writer, boolean autoFlush, Console console)
int	ExpressionDataFileServiceImpl.writeCellBrowserSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useBioAssayIds, boolean useRawColumnNames, int fetchSize, boolean useCursorFetchIfSupported, Writer writer, boolean autoFlush, Console console)
void	ExpressionDataFileService.writeDesignMatrix(ExpressionExperiment ee, boolean useProcessedData, Writer writer, boolean autoFlush)	Writes out the experimental design for the given experiment.
void	ExpressionDataFileService.writeDesignMatrix(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType, Writer writer, boolean autoFlush)	Writes out the experimental design for the given experiment and quantitation type.
void	ExpressionDataFileServiceImpl.writeDesignMatrix(ExpressionExperiment ee, boolean useProcessedData, Writer writer, boolean autoFlush)
void	ExpressionDataFileServiceImpl.writeDesignMatrix(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType, Writer writer, boolean autoFlush)
Collection<Path>	ExpressionDataFileService.writeDiffExAnalysisArchiveFiles(ExpressionExperiment ee, Path outputDir, boolean forceWrite)	Write all the differential expression data files for a given experiment to a particular directory.
Collection<Path>	ExpressionDataFileServiceImpl.writeDiffExAnalysisArchiveFiles(ExpressionExperiment ee, Path outputDir, boolean forceWrite)
int	ExpressionDataFileService.writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Path destDir, boolean autoFlush, Console console)
int	ExpressionDataFileService.writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, OutputStream stream)
int	ExpressionDataFileService.writeMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Path destDir, boolean autoFlush, Console console)	Write single-cell expression data to a given output stream for a given quantitation type.
int	ExpressionDataFileService.writeMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, OutputStream stream)	Write single-cell expression data to a given output stream for a given quantitation type.
int	ExpressionDataFileServiceImpl.writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Path destDir, boolean autoFlush, Console console)
int	ExpressionDataFileServiceImpl.writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, OutputStream stream)
int	ExpressionDataFileServiceImpl.writeMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Path destDir, boolean autoFlush, Console console)
int	ExpressionDataFileServiceImpl.writeMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, OutputStream stream)
Optional<LockedPath>	ExpressionDataFileService.writeOrLocateDesignFile(ExpressionExperiment ee, boolean useProcessedQuantitationType, boolean forceWrite)	Locate or create an experimental design file for a given experiment.
Optional<LockedPath>	ExpressionDataFileService.writeOrLocateDesignFile(ExpressionExperiment ee, boolean useProcessedQuantitationType, boolean forceWrite, long timeout, TimeUnit timeUnit)
Optional<LockedPath>	ExpressionDataFileServiceImpl.writeOrLocateDesignFile(ExpressionExperiment ee, boolean useProcessedData, boolean forceWrite)
Optional<LockedPath>	ExpressionDataFileServiceImpl.writeOrLocateDesignFile(ExpressionExperiment ee, boolean useProcessedData, boolean forceWrite, long timeout, TimeUnit timeUnit)
Collection<Path>	ExpressionDataFileService.writeOrLocateDiffExAnalysisArchiveFiles(ExpressionExperiment ee, boolean forceWrite)	Locate or create the differential expression archive file(s) for a given experiment.
Collection<Path>	ExpressionDataFileServiceImpl.writeOrLocateDiffExAnalysisArchiveFiles(ExpressionExperiment ee, boolean forceWrite)
Optional<LockedPath>	ExpressionDataFileService.writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean filtered, boolean forceWrite)
Optional<LockedPath>	ExpressionDataFileServiceImpl.writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean filtered, boolean forceWrite)
LockedPath	ExpressionDataFileService.writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
LockedPath	ExpressionDataFileServiceImpl.writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
LockedPath	ExpressionDataFileService.writeOrLocateMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Console console)	Write single-cell expression data to a standard location for a given quantitation type.
LockedPath	ExpressionDataFileServiceImpl.writeOrLocateMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Console console)
Future<Path>	ExpressionDataFileService.writeOrLocateMexSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite)
Future<Path>	ExpressionDataFileServiceImpl.writeOrLocateMexSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite)
Optional<LockedPath>	ExpressionDataFileService.writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean filtered, boolean forceWrite)	Locate or create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).
Optional<LockedPath>	ExpressionDataFileService.writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean filtered, boolean forceWrite, long timeout, TimeUnit timeUnit)
Optional<LockedPath>	ExpressionDataFileServiceImpl.writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean filtered, boolean forceWrite)
Optional<LockedPath>	ExpressionDataFileServiceImpl.writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean filtered, boolean forceWrite, long timeout, TimeUnit timeUnit)
Future<Path>	ExpressionDataFileService.writeOrLocateProcessedDataFileAsync(ExpressionExperiment ee, boolean filtered, boolean forceWrite)	Build the processed-expression data file off the request thread via the expressionDataFileTaskExecutor.
Future<Path>	ExpressionDataFileServiceImpl.writeOrLocateProcessedDataFileAsync(ExpressionExperiment ee, boolean filtered, boolean forceWrite)
LockedPath	ExpressionDataFileService.writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)	Locate or create a new data file for the given quantitation type.
LockedPath	ExpressionDataFileService.writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType qt, boolean forceWrite, long timeout, TimeUnit timeUnit)
LockedPath	ExpressionDataFileServiceImpl.writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
LockedPath	ExpressionDataFileServiceImpl.writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite, long timeout, TimeUnit timeUnit)
Future<Path>	ExpressionDataFileService.writeOrLocateRawExpressionDataFileAsync(ExpressionExperiment ee, QuantitationType qt, boolean forceWrite)	Build the raw-expression data file off the request thread via the expressionDataFileTaskExecutor.
Future<Path>	ExpressionDataFileServiceImpl.writeOrLocateRawExpressionDataFileAsync(ExpressionExperiment ee, QuantitationType qt, boolean forceWrite)
LockedPath	ExpressionDataFileService.writeOrLocateTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Console console)	Write single-cell expression data to a standard location for a given quantitation type in tabular format.
LockedPath	ExpressionDataFileServiceImpl.writeOrLocateTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Console console)
Future<Path>	ExpressionDataFileService.writeOrLocateTabularSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite)
Future<Path>	ExpressionDataFileServiceImpl.writeOrLocateTabularSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite)
int	ExpressionDataFileService.writeProcessedExpressionData(ExpressionExperiment ee, boolean filtered, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)	Write processed expression data to a given writer for a given quantitation type.
int	ExpressionDataFileService.writeProcessedExpressionData(ExpressionExperiment ee, List<BioAssay> samples, boolean filtered, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeProcessedExpressionData(ExpressionExperiment ee, boolean filtered, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeProcessedExpressionData(ExpressionExperiment ee, List<BioAssay> samples, boolean filtered, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeRawExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)	Write raw expression data to a given writer for a given quantitation type.
int	ExpressionDataFileServiceImpl.writeRawExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeTabularSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useBioAssayIds, boolean useRawColumnNames, int fetchSize, boolean useCursorFetchIfSupported, Writer writer, boolean autoFlush, Console console)
int	ExpressionDataFileService.writeTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useBioAssayIds, boolean useRawColumnNames, int fetchSize, boolean useCursorFetchIfSupported, Writer writer, boolean autoFlush, Console console)	Write single-cell expression data to a given writer for a given quantitation type in tabular format.
int	ExpressionDataFileServiceImpl.writeTabularSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useBioAssayIds, boolean useRawColumnNames, int fetchSize, boolean useCursorFetchIfSupported, Writer writer, boolean autoFlush, Console console)
int	ExpressionDataFileServiceImpl.writeTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useBioAssayIds, boolean useRawColumnNames, int fetchSize, boolean useCursorFetchIfSupported, Writer writer, boolean autoFlush, Console console)

Uses of ExpressionExperiment in ubic.gemma.core.analysis.singleCell.aggregate

Methods in ubic.gemma.core.analysis.singleCell.aggregate with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
QuantitationType	SingleCellExpressionExperimentAggregateService.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic, FactorValue> cellTypeMapping, SingleCellAggregationConfig config)	Aggregate preferred single-cell data vectors by the given cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentAggregateServiceImpl.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic, FactorValue> cellType2Factor, SingleCellAggregationConfig config)
QuantitationType	SingleCellExpressionExperimentAggregateService.aggregateVectorsByCellType(ExpressionExperiment ee, List<BioAssay> cellBAs, SingleCellAggregationConfig config)	Aggregate preferred single-cell data vectors by the preferred cell type assignment and the only cell type factor of the experiment.
QuantitationType	SingleCellExpressionExperimentAggregateServiceImpl.aggregateVectorsByCellType(ExpressionExperiment ee, List<BioAssay> cellBAs, SingleCellAggregationConfig config)
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetService.createSubSets(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> cellTypeMapping, SingleCellExperimentSubSetsCreationConfig config)	Subset biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetServiceImpl.createSubSets(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> mappedCellTypeFactors, SingleCellExperimentSubSetsCreationConfig config)
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.createSubSetsAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics cta, ExperimentalFactor cellTypeFactor, Map<Characteristic, FactorValue> c2f, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	Create subsets and aggregate by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.createSubSetsAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor cellTypeFactor, Map<Characteristic, FactorValue> c2f, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	See SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.createSubSetsAndAggregateByCellType(ExpressionExperiment, SingleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig) for why this is Propagation.NEVER.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.createSubSetsAndAggregateByCellType(ExpressionExperiment expressionExperiment, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	Create subsets and aggregate by cell type.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.createSubSetsAndAggregateByCellType(ExpressionExperiment expressionExperiment, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	Not transactional: SingleCellExpressionExperimentSubSetService.createSubSets(ExpressionExperiment, SingleCellDimension, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellExperimentSubSetsCreationConfig) commits the subset/BioAssay/BioMaterial rows it creates — and with them the ACL rows AclEventListener inserts alongside each — BEFORE SingleCellExpressionExperimentAggregateService.aggregateVectors(ExpressionExperiment, QuantitationType, List, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellAggregationConfig) opens its own, separate, potentially hour-long transaction to stream and aggregate the single-cell data.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetService.createSubSetsByCellType(ExpressionExperiment ee, SingleCellExperimentSubSetsCreationConfig config)	Subset a single-cell dataset by preferred cell type assignment the cell type factor and the
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetServiceImpl.createSubSetsByCellType(ExpressionExperiment ee, SingleCellExperimentSubSetsCreationConfig config)
boolean	SingleCellExpressionExperimentAggregateService.isAggregated(ExpressionExperiment ee, QuantitationType quantitationType)	Check if a particular quantitation type is aggregated.
boolean	SingleCellExpressionExperimentAggregateServiceImpl.isAggregated(ExpressionExperiment ee, QuantitationType quantitationType)
void	SingleCellExpressionExperimentAggregateAuditService.recordAggregateCreated(ExpressionExperiment ee, String note, SingleCellAggregationPayload payload)	Emit a DataAddedEvent for ee with the given aggregate payload.
void	SingleCellExpressionExperimentAggregateAuditServiceImpl.recordAggregateCreated(ExpressionExperiment ee, String note, SingleCellAggregationPayload payload)
void	SingleCellExpressionExperimentSubSetAuditService.recordSubSetsCreated(ExpressionExperiment ee, String note, SingleCellSubSetsCreatedPayload payload)	Emit a SingleCellSubSetsCreatedEvent for ee carrying the typed SingleCellSubSetsCreatedPayload.
void	SingleCellExpressionExperimentSubSetAuditServiceImpl.recordSubSetsCreated(ExpressionExperiment ee, String note, SingleCellSubSetsCreatedPayload payload)
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)	Re-aggregate a dataset by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.redoAggregateByCellType(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)	Re-aggregate a dataset by cell type.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.redoAggregateByCellType(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)
int	SingleCellExpressionExperimentAggregateService.removeAggregatedVectors(ExpressionExperiment ee, QuantitationType qt)	Remove aggregated vectors for the given quantitation type.
int	SingleCellExpressionExperimentAggregateService.removeAggregatedVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)	Remove aggregated vectors for the given quantitation type.
int	SingleCellExpressionExperimentAggregateServiceImpl.removeAggregatedVectors(ExpressionExperiment ee, QuantitationType qt)
int	SingleCellExpressionExperimentAggregateServiceImpl.removeAggregatedVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)

Uses of ExpressionExperiment in ubic.gemma.core.datastructure.matrix

Methods in ubic.gemma.core.datastructure.matrix that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	AbstractBulkExpressionDataMatrix.getExpressionExperiment()
ExpressionExperiment	AbstractMultiAssayExpressionDataMatrix.getExpressionExperiment()
ExpressionExperiment	EmptySingleCellExpressionDataMatrix.getExpressionExperiment()
ExpressionExperiment	ExpressionDataMatrix.getExpressionExperiment()	Return the expression experiment this matrix is holding data for, if known.
ExpressionExperiment	MaskedExpressionDataMatrix.getExpressionExperiment()
ExpressionExperiment	SingleCellExpressionDataDoubleMatrix.getExpressionExperiment()
ExpressionExperiment	SingleCellExpressionDataIntMatrix.getExpressionExperiment()
ExpressionExperiment	TwoChannelExpressionDataMatrixBuilder.getExpressionExperiment()	Deprecated.

Methods in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
static Collection<QuantitationType>	TwoChannelExpressionDataMatrixBuilder.getMissingValueQuantitationTypes(ExpressionExperiment expressionExperiment)	Deprecated.
static Collection<QuantitationType>	TwoChannelExpressionDataMatrixBuilder.getPreferredAndMissingQuantitationTypes(ExpressionExperiment expressionExperiment)	Deprecated.
static Collection<QuantitationType>	TwoChannelExpressionDataMatrixBuilder.getPreferredQuantitationTypes(ExpressionExperiment expressionExperiment)	Deprecated.
static Collection<QuantitationType>	TwoChannelExpressionDataMatrixBuilder.getUsefulQuantitationTypes(ExpressionExperiment expressionExperiment)	Deprecated.

Constructors in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionExperiment

Modifier	Constructor	Description
protected	AbstractBulkExpressionDataMatrix(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType quantitationType, List<CompositeSequence> designElements)
protected	AbstractMultiAssayExpressionDataMatrix(ExpressionExperiment ee)	Create a simple multi-assay matrix.
protected	AbstractMultiAssayExpressionDataMatrix(ExpressionExperiment ee, Collection<BioAssayDimension> dimension)
	EmptyBulkExpressionDataMatrix(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType quantitationType)
	EmptyExpressionMatrix(ExpressionExperiment ee, Collection<BioAssayDimension> dims)
	EmptyExpressionMatrix(ExpressionExperiment ee, BioAssayDimension ba)
	EmptySingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, SingleCellDimension dimension, QuantitationType quantitationType)
	ExpressionDataBooleanMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors)
	ExpressionDataBooleanMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors, List<QuantitationType> qtypes)
	ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors)
	ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> dataVectors, Collection<QuantitationType> quantitationTypes)
	ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> dataVectors, QuantitationType quantitationType)
	ExpressionDataDoubleMatrix(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, BioMaterial> dataMatrix, QuantitationType qt)	Create a matrix given a 'raw' matrix that uses the same samples as the experiment.
	ExpressionDataIntegerMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors)
	ExpressionDataStringMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors)
	SingleCellExpressionDataDoubleMatrix(ExpressionExperiment ee, QuantitationType quantitationType, SingleCellDimension dimension, List<CompositeSequence> designElements, no.uib.cipr.matrix.sparse.CompRowMatrix matrix)

Uses of ExpressionExperiment in ubic.gemma.core.datastructure.matrix.io

Methods in ubic.gemma.core.datastructure.matrix.io with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
static void	ExpressionDataWriterUtils.appendBaseHeader(ExpressionExperiment experiment, String fileTypeStr, String experimentUrl, BuildInfo buildInfo, Date timestamp, Writer buf)	Appends base header information (about the experiment) to a file.
static void	ExpressionDataWriterUtils.appendBaseHeader(ExpressionExperiment experiment, QuantitationType quantitationType, Class<? extends DataVector> dataVectorType, String fileTypeStr, String experimentUrl, BuildInfo buildInfo, Date timestamp, Writer buf)	Append base header information (about the experiment) to a file with some information about the quantitation type.
void	ExperimentalDesignWriter.write(ExpressionExperiment ee, Writer writer)	Write the experimental design of the given ExpressionExperiment to the given Writer.
void	ExperimentalDesignWriter.write(ExpressionExperiment ee, QuantitationType quantitationType, Class<? extends DataVector> vectorType, Collection<BioAssay> bioAssays, boolean writeBaseHeader, Writer writer)	Write the experimental design of the given ExpressionExperiment to the given Writer for a given collection of assays.
void	MeanVarianceWriter.write(ExpressionExperiment ee, QuantitationType qt, Writer writer)

Uses of ExpressionExperiment in ubic.gemma.core.loader.entrez.pubmed

Methods in ubic.gemma.core.loader.entrez.pubmed with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
BibliographicReference	ExpressionExperimentBibRefFinder.locatePrimaryReference(ExpressionExperiment ee)
BibliographicReference	ExpressionExperimentBibRefFinder.locatePrimaryReference(ExpressionExperiment ee, boolean forceFromGeo)	Locate the primary reference for an experiment from GEO.

Uses of ExpressionExperiment in ubic.gemma.core.loader.expression

Methods in ubic.gemma.core.loader.expression with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	DataUpdater.addAffyDataFromAPTOutput(ExpressionExperiment ee, String pathToAptOutputFile)
void	DataUpdaterImpl.addAffyDataFromAPTOutput(ExpressionExperiment ee, String pathToAptOutputFile)	Affymetrix: Use to bypass the automated running of apt-probeset-summarize.
void	DataUpdater.addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Map<BioAssay, SequencingMetadata> sequencingMetadata, boolean allowMissingSamples)
void	DataUpdaterImpl.addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Map<BioAssay, SequencingMetadata> sequencingMetadata, boolean allowMissingSamples)	RNA-seq: Replaces data.
void	DataUpdater.addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	DataUpdaterImpl.addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)	Generic but in practice used for RNA-seq.
ArrayDesign	ExpressionExperimentPlatformSwitchService.locateMergedDesign(ExpressionExperiment expExp)
void	DataUpdater.log2cpmFromCounts(ExpressionExperiment ee, QuantitationType qt)
void	DataUpdaterImpl.log2cpmFromCounts(ExpressionExperiment ee, QuantitationType qt)	RNA-seq: For back filling log2cpm when only counts are available.
void	DataUpdaterAuditService.recordDataReplaced(ExpressionExperiment ee, String note)	Record a DataReplacedEvent against the given experiment with the supplied note.
void	DataUpdaterAuditServiceImpl.recordDataReplaced(ExpressionExperiment ee, String note)	Record a DataReplacedEvent against the given experiment with the supplied note.
void	DataUpdaterAuditService.recordPlatformSwitch(ExpressionExperiment ee, String note)	Record an ExpressionExperimentPlatformSwitchEvent against the given experiment with the supplied note.
void	DataUpdaterAuditServiceImpl.recordPlatformSwitch(ExpressionExperiment ee, String note)	Record an ExpressionExperimentPlatformSwitchEvent against the given experiment with the supplied note.
void	DataUpdater.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	DataUpdater.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)
void	DataUpdaterImpl.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)	Replace the data associated with the experiment (or add it if there is none).
void	DataUpdaterImpl.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)	Replace the data associated with the experiment (or add it if there is none).
void	DataUpdater.reprocessAffyDataFromCel(ExpressionExperiment ee)
void	DataUpdaterImpl.reprocessAffyDataFromCel(ExpressionExperiment ee)	Affymetrix only: Provide or replace data for an Affymetrix-based experiment, using CEL files.
void	ExpressionExperimentPlatformSwitchService.switchExperimentToArrayDesign(ExpressionExperiment ee, ArrayDesign arrayDesign)	If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatform
ArrayDesign	ExpressionExperimentPlatformSwitchService.switchExperimentToMergedPlatform(ExpressionExperiment expExp)	Automatically identify an appropriate merged platform
boolean	ExpressionExperimentPlatformSwitchService.switchPlatformAndVectors(ExpressionExperiment ee, ArrayDesign arrayDesign)	The transactional part of ExpressionExperimentPlatformSwitchService.switchExperimentToArrayDesign(ExpressionExperiment, ArrayDesign): everything except regenerating the processed vectors.

Constructors in ubic.gemma.core.loader.expression with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	RawDataPostprocessingException(ExpressionExperiment ee, String rawDataChange, Throwable cause)

Uses of ExpressionExperiment in ubic.gemma.core.loader.expression.arrayDesign

Methods in ubic.gemma.core.loader.expression.arrayDesign with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
static Map<BioAssay,String>	AffyChipTypeExtractor.getChipTypes(ExpressionExperiment ee, Collection<File> files)	Extract a string like "Rat230_2" from CEL files.

Uses of ExpressionExperiment in ubic.gemma.core.loader.expression.cellxgene

Methods in ubic.gemma.core.loader.expression.cellxgene that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	CellXGeneConverter.convert(CollectionMetadata collectionMetadata, DatasetMetadata datasetMetadata, DatasetVersion datasetVersion, ArrayDesign platform, Collection<CompositeSequence> compositeSequences, String datasetShortName, SingleCellDataLoader dataLoader, boolean loadSingleCellData)
ExpressionExperiment	CellXGeneDataLoaderService.fetchAndLoad(String collectionId, String datasetId, String assetId, ArrayDesign platform, String datasetShortName, boolean loadSingleCellData, boolean keepPooledSample, boolean keepUnknownSample, boolean dryRun)	Fetch a CELLxGENE dataset and load it into the database.
ExpressionExperiment	CellXGeneDataLoaderServiceImpl.fetchAndLoad(String collectionId, String datasetId, String assetId, ArrayDesign platform, String datasetShortName, boolean loadSingleCellData, boolean keepPooledSample, boolean keepUnknownSample, boolean dryRun)

Methods in ubic.gemma.core.loader.expression.cellxgene with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
DatabaseEntry	CellXGeneDataLoaderService.replaceVersionAccession(ExpressionExperiment ee, String datasetId)	Replace a CELLxGENE accession that holds a dataset version ID by one that holds the permanent dataset ID.
DatabaseEntry	CellXGeneDataLoaderServiceImpl.replaceVersionAccession(ExpressionExperiment ee, String datasetId)

Uses of ExpressionExperiment in ubic.gemma.core.loader.expression.geo

Methods in ubic.gemma.core.loader.expression.geo that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	GeoConverter.convert(GeoDataset geoDataset, boolean skipDataVectors)
ExpressionExperiment	GeoConverterImpl.convert(GeoDataset geoDataset, boolean skipDataVectors)

Methods in ubic.gemma.core.loader.expression.geo that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	GeoConverter.convert(GeoSeries geoSeries)
Collection<ExpressionExperiment>	GeoConverter.convert(GeoSeries geoSeries, boolean skipDataVectors)
Collection<ExpressionExperiment>	GeoConverterImpl.convert(GeoSeries geoSeries)
Collection<ExpressionExperiment>	GeoConverterImpl.convert(GeoSeries geoSeries, boolean skipDataVectors)

Methods in ubic.gemma.core.loader.expression.geo with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	GeoConverter.convertSubsetToExperimentalFactor(ExpressionExperiment expExp, GeoSubset geoSubSet)	Converts Geo subsets to experimental factors.
void	GeoConverterImpl.convertSubsetToExperimentalFactor(ExpressionExperiment expExp, GeoSubset geoSubSet)

Uses of ExpressionExperiment in ubic.gemma.core.loader.expression.geo.service

Methods in ubic.gemma.core.loader.expression.geo.service with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	GeoUpdateAuditService.recordGeoUpdate(ExpressionExperiment ee, int numNewCharacteristics, boolean pubUpdate)	Record an ExpressionExperimentUpdateFromGEOEvent audit row for ee, but only when the update actually changed something -- either a new characteristic was added or the primary publication was populated.
void	GeoUpdateAuditServiceImpl.recordGeoUpdate(ExpressionExperiment ee, int numNewCharacteristics, boolean pubUpdate)
void	GeoService.updateFromGEO(ExpressionExperiment expressionExperiment, GeoService.GeoUpdateConfig geoUpdateConfig)	Refetch and reprocess a given experiment.
void	GeoServiceImpl.updateFromGEO(ExpressionExperiment ee, GeoService.GeoUpdateConfig geoUpdateConfig)

Uses of ExpressionExperiment in ubic.gemma.core.loader.expression.simple

Methods in ubic.gemma.core.loader.expression.simple that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	SimpleExpressionDataLoaderService.convert(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> data)	Convert simple experiment metadata and data into Gemma objects.
ExpressionExperiment	SimpleExpressionDataLoaderServiceImpl.convert(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> matrix)
ExpressionExperiment	SimpleExpressionDataLoaderService.create(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> data)	Parses, converts (into Gemma objects), and loads data into the database.
ExpressionExperiment	SimpleExpressionDataLoaderServiceImpl.create(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> matrix)

Methods in ubic.gemma.core.loader.expression.simple with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	ExperimentalDesignImporter.importDesign(ExpressionExperiment experiment, InputStream is)	This is the main builder director method of the application: It processes the input file containing information about the experimental design for a given expression experiment.
void	ExperimentalDesignImporterImpl.importDesign(ExpressionExperiment experiment, InputStream is)

Uses of ExpressionExperiment in ubic.gemma.core.loader.expression.singleCell

Methods in ubic.gemma.core.loader.expression.singleCell with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
Path	SingleCellDataLoaderServiceImpl.getSeuratDiskFile(ExpressionExperiment ee)
QuantitationType	SingleCellDataLoaderService.load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataLoaderConfig config)	Load single-cell data, the data type is automatically detected.
QuantitationType	SingleCellDataLoaderService.load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load a specific single-cell data type.
QuantitationType	SingleCellDataLoaderServiceImpl.load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataLoaderConfig config)
QuantitationType	SingleCellDataLoaderServiceImpl.load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataType dataType, SingleCellDataLoaderConfig config)
Collection<CellTypeAssignment>	SingleCellDataLoaderService.loadCellTypeAssignments(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load the cell type assignments, the data type is automatically detected.
Collection<CellTypeAssignment>	SingleCellDataLoaderService.loadCellTypeAssignments(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load the cell type assignments.
Collection<CellTypeAssignment>	SingleCellDataLoaderServiceImpl.loadCellTypeAssignments(ExpressionExperiment ee, SingleCellDataLoaderConfig config)
Collection<CellTypeAssignment>	SingleCellDataLoaderServiceImpl.loadCellTypeAssignments(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)
Collection<CellLevelCharacteristics>	SingleCellDataLoaderService.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e.
Collection<CellLevelCharacteristics>	SingleCellDataLoaderService.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e.
Collection<CellLevelCharacteristics>	SingleCellDataLoaderServiceImpl.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataLoaderConfig config)
Collection<CellLevelCharacteristics>	SingleCellDataLoaderServiceImpl.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)
Map<BioAssay, SequencingMetadata>	SingleCellDataLoaderService.loadSequencingMetadata(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load sequencing metadata.
Map<BioAssay, SequencingMetadata>	SingleCellDataLoaderServiceImpl.loadSequencingMetadata(ExpressionExperiment ee, SingleCellDataLoaderConfig config)

Uses of ExpressionExperiment in ubic.gemma.core.search

Methods in ubic.gemma.core.search that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
default Collection<SearchResult<ExpressionExperiment>>	SearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)

Uses of ExpressionExperiment in ubic.gemma.core.search.source

Methods in ubic.gemma.core.search.source that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Collection<SearchResult<ExpressionExperiment>>	CompositeSearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperiment>>	DatabaseSearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperiment>>	HibernateSearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperiment>>	OntologySearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)	Search via characteristics i.e.

Uses of ExpressionExperiment in ubic.gemma.core.tasks.analysis.diffex

Methods in ubic.gemma.core.tasks.analysis.diffex that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	DifferentialExpressionAnalysisTaskCommand.getExpressionExperiment()

Methods in ubic.gemma.core.tasks.analysis.diffex with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisTaskCommand.setExpressionExperiment(ExpressionExperiment expressionExperiment)

Constructors in ubic.gemma.core.tasks.analysis.diffex with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	DifferentialExpressionAnalysisRemoveTaskCommand(ExpressionExperiment ee, DifferentialExpressionAnalysis toRemove)
	DifferentialExpressionAnalysisTaskCommand(boolean forceAnalysis, ExpressionExperiment expressionExperiment)
	DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment ee)
	DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment ee, DifferentialExpressionAnalysis toRedo)

Uses of ExpressionExperiment in ubic.gemma.core.tasks.analysis.expression

Methods in ubic.gemma.core.tasks.analysis.expression that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	ExpressionExperimentPlatformSwitchTaskCommand.getExpressionExperiment()
ExpressionExperiment	GeeqTaskCommand.getExpressionExperiment()
ExpressionExperiment	PreprocessTaskCommand.getExpressionExperiment()
ExpressionExperiment	SvdTaskCommand.getExpressionExperiment()
ExpressionExperiment	TwoChannelMissingValueTaskCommand.getExpressionExperiment()	Deprecated.

Methods in ubic.gemma.core.tasks.analysis.expression with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	ExpressionExperimentPlatformSwitchTaskCommand.setExpressionExperiment(ExpressionExperiment expressionExperiment)
void	GeeqTaskCommand.setExpressionExperiment(ExpressionExperiment expressionExperiment)
void	PreprocessTaskCommand.setExpressionExperiment(ExpressionExperiment expressionExperiment)
void	SvdTaskCommand.setExpressionExperiment(ExpressionExperiment expressionExperiment)
void	TwoChannelMissingValueTaskCommand.setExpressionExperiment(ExpressionExperiment expressionExperiment)	Deprecated.

Constructors in ubic.gemma.core.tasks.analysis.expression with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	BatchInfoFetchTaskCommand(ExpressionExperiment expressionExperiment)
	ExpressionExperimentPlatformSwitchTaskCommand(ExpressionExperiment expressionExperiment, ArrayDesign targetArrayDesign)
	GeeqTaskCommand(ExpressionExperiment expressionExperiment, GeeqService.ScoreMode mode)
	PreprocessTaskCommand(ExpressionExperiment ee)
	SvdTaskCommand(ExpressionExperiment expressionExperiment)
	SvdTaskCommand(ExpressionExperiment expressionExperiment, boolean postProcessOnly)
	TwoChannelMissingValueTaskCommand(ExpressionExperiment ee)	Deprecated.
	TwoChannelMissingValueTaskCommand(ExpressionExperiment expressionExperiment, double s2n, Collection<Double> extraMissingValueIndictors)	Deprecated.

Uses of ExpressionExperiment in ubic.gemma.core.tasks.maintenance

Methods in ubic.gemma.core.tasks.maintenance that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	ExpressionExperimentReportTaskCommand.getExpressionExperiment()

Methods in ubic.gemma.core.tasks.maintenance with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	ExpressionExperimentReportTaskCommand.setExpressionExperiment(ExpressionExperiment expressionExperiment)

Constructors in ubic.gemma.core.tasks.maintenance with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	ExpressionExperimentReportTaskCommand(ExpressionExperiment expressionExperiment)

Uses of ExpressionExperiment in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	SingleCellSparsityHeatmap.getExpressionExperiment()

Methods in ubic.gemma.core.visualization with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, Slice<CompositeSequence> designElements, List<Gene> genes)	Create a heatmap for a given set of design elements.
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromVectors(ExpressionExperiment ee, BioAssayDimension dimension, Slice<? extends BulkExpressionDataVector> vectors, List<Gene> genes)	Create a heatmap for a given set of vectors.

Constructors in ubic.gemma.core.visualization with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	SingleCellSparsityHeatmap(ExpressionExperiment expressionExperiment, SingleCellDimension singleCellDimension, BioAssayDimension dimension, Collection<ExpressionExperimentSubSet> subSets, Map<BioAssay,Long> designElementsPerSample, SingleCellSparsityHeatmap.SingleCellHeatmapType type)

Uses of ExpressionExperiment in ubic.gemma.core.visualization.cellbrowser

Methods in ubic.gemma.core.visualization.cellbrowser with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
static String	CellBrowserUtils.constructDatasetName(ExpressionExperiment ee)
String	CellBrowserService.getBrowserUrl(ExpressionExperiment ee)	Obtain a URL for the Cell Browser for a given ExpressionExperiment.
String	CellBrowserServiceImpl.getBrowserUrl(ExpressionExperiment ee)
boolean	CellBrowserService.hasBrowser(ExpressionExperiment ee)	Check if a particular ExpressionExperiment has a Cell Browser dataset configured.
boolean	CellBrowserServiceImpl.hasBrowser(ExpressionExperiment ee)
void	CellBrowserMetadataWriter.write(ExpressionExperiment ee, SingleCellDimension singleCellDimension, Writer writer)

Uses of ExpressionExperiment in ubic.gemma.model.analysis

Classes in ubic.gemma.model.analysis that implement interfaces with type arguments of type ExpressionExperiment

Modifier and Type	Class	Description
class	SingleExperimentAnalysis<T extends BioAssaySet>	An analysis of a single experiment or subset.

Methods in ubic.gemma.model.analysis that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	SingleExperimentAnalysis.getSecurityOwner()	Experiment analysis are always owned by the experiment (or source experiment, if a subset).

Uses of ExpressionExperiment in ubic.gemma.model.analysis.expression

Methods in ubic.gemma.model.analysis.expression that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Set<ExpressionExperiment>	ExpressionExperimentSet.getExperiments()

Method parameters in ubic.gemma.model.analysis.expression with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
void	ExpressionExperimentSet.setExperiments(Set<ExpressionExperiment> experiments)

Uses of ExpressionExperiment in ubic.gemma.model.analysis.expression.coexpression

Subclasses with type arguments of type ExpressionExperiment in ubic.gemma.model.analysis.expression.coexpression

Modifier and Type	Class	Description
class	SampleCoexpressionAnalysis	The 'analysis' in the name is a bit of a stretch here, as this object servers purely as an aggregator of all the sample coexpression matrices.

Methods in ubic.gemma.model.analysis.expression.coexpression with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
static SampleCoexpressionAnalysis	SampleCoexpressionAnalysis.Factory.newInstance(ExpressionExperiment experimentAnalyzed, SampleCoexpressionMatrix fullCoexpressionMatrix, SampleCoexpressionMatrix regressedCoexpressionMatrix)

Uses of ExpressionExperiment in ubic.gemma.model.analysis.expression.pca

Subclasses with type arguments of type ExpressionExperiment in ubic.gemma.model.analysis.expression.pca

Modifier and Type	Class	Description
class	PrincipalComponentAnalysis

Uses of ExpressionExperiment in ubic.gemma.model.common.description

Methods in ubic.gemma.model.common.description that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	AnnotationRelation.getExpressionExperiment()

Methods in ubic.gemma.model.common.description with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	AnnotationRelation.setExpressionExperiment(ExpressionExperiment expressionExperiment)

Uses of ExpressionExperiment in ubic.gemma.model.common.quantitationtype

Constructors in ubic.gemma.model.common.quantitationtype with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	QuantitationTypeValueObject(QuantitationType qt, ExpressionExperiment expressionExperiment, Class<? extends DataVector> vectorType)	Create a QuantitationType VO in the context of an associated experiment.

Uses of ExpressionExperiment in ubic.gemma.model.common.search

Methods in ubic.gemma.model.common.search that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	SearchSettings.getDatasetConstraint()	Constraint results to be related to the given dataset.

Methods in ubic.gemma.model.common.search with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
SearchSettings.SearchSettingsBuilder	SearchSettings.SearchSettingsBuilder.datasetConstraint(ExpressionExperiment datasetConstraint)	Constraint results to be related to the given dataset.
void	SearchSettings.setDatasetConstraint(ExpressionExperiment datasetConstraint)	Constraint results to be related to the given dataset.
SearchSettings	SearchSettings.withDatasetConstraint(ExpressionExperiment datasetConstraint)	Constraint results to be related to the given dataset.

Uses of ExpressionExperiment in ubic.gemma.model.expression.bioAssay

Classes in ubic.gemma.model.expression.bioAssay that implement interfaces with type arguments of type ExpressionExperiment

Modifier and Type	Class	Description
class	BioAssay	Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).

Methods in ubic.gemma.model.expression.bioAssay that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	BioAssay.getSecurityOwner()

Methods in ubic.gemma.model.expression.bioAssay with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	BioAssay.setSecurityOwner(ExpressionExperiment securable)

Uses of ExpressionExperiment in ubic.gemma.model.expression.bioAssayData

Classes in ubic.gemma.model.expression.bioAssayData that implement interfaces with type arguments of type ExpressionExperiment

Modifier and Type	Class	Description
class	MeanVarianceRelation

Methods in ubic.gemma.model.expression.bioAssayData that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	CellTypeAssignment.getExperimentAnalyzed()	The experiment whose cells this assigns, in the EXPERIMENT_ANALYZED_FK column every other analysis in ANALYSIS uses for the same fact (Paul, 2026-09-14).
ExpressionExperiment	DataVector.getExpressionExperiment()
ExpressionExperiment	SingleCellDimensionExperiment.getExpressionExperiment()
ExpressionExperiment	MeanVarianceRelation.getSecurityOwner()

Methods in ubic.gemma.model.expression.bioAssayData with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
static Consumer<SingleCellExpressionDataVector>	SingleCellExpressionDataVectorUtils.createStreamMonitor(ExpressionExperiment ee, QuantitationType qt, String logCategory, int reportFrequency, long numVecs, Console console)	Create a consumer for a Stream that will report progress of retrieving single-cell vectors.
void	CellTypeAssignment.setExperimentAnalyzed(ExpressionExperiment experimentAnalyzed)	The experiment whose cells this assigns, in the EXPERIMENT_ANALYZED_FK column every other analysis in ANALYSIS uses for the same fact (Paul, 2026-09-14).
void	DataVector.setExpressionExperiment(ExpressionExperiment expressionExperiment)
void	SingleCellDimensionExperiment.setExpressionExperiment(ExpressionExperiment expressionExperiment)
void	MeanVarianceRelation.setSecurityOwner(ExpressionExperiment ee)

Uses of ExpressionExperiment in ubic.gemma.model.expression.biomaterial

Classes in ubic.gemma.model.expression.biomaterial that implement interfaces with type arguments of type ExpressionExperiment

Modifier and Type	Class	Description
class	BioMaterial	In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...

Methods in ubic.gemma.model.expression.biomaterial that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	BioMaterial.getSecurityOwner()

Methods in ubic.gemma.model.expression.biomaterial with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	BioMaterial.setSecurityOwner(ExpressionExperiment securityOwner)

Uses of ExpressionExperiment in ubic.gemma.model.expression.experiment

Subclasses with type arguments of type ExpressionExperiment in ubic.gemma.model.expression.experiment

Modifier and Type	Class	Description
class	ExpressionExperimentValueObject

Classes in ubic.gemma.model.expression.experiment that implement interfaces with type arguments of type ExpressionExperiment

Modifier and Type	Class	Description
class	ExperimentalDesign	Hibernate Search 7 mapping: indexed root and embedded contributor to ExpressionExperiment.getExperimentalDesign().
class	ExperimentalFactor	ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
class	ExpressionExperimentSubSet	A subset of assays (or derived assays) from an ExpressionExperiment.
class	FactorValue	The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"

Methods in ubic.gemma.model.expression.experiment that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	ExperimentalDesign.getSecurityOwner()
ExpressionExperiment	ExperimentalFactor.getSecurityOwner()
ExpressionExperiment	ExpressionExperimentSubSet.getSecurityOwner()
ExpressionExperiment	FactorValue.getSecurityOwner()
ExpressionExperiment	ExpressionExperimentSubSet.getSourceExperiment()
static ExpressionExperiment	ExpressionExperiment.Factory.newInstance()

Methods in ubic.gemma.model.expression.experiment that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Set<ExpressionExperiment>	ExpressionExperiment.getOtherParts()

Methods in ubic.gemma.model.expression.experiment with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
static ExpressionExperimentSubSet	ExpressionExperimentSubSet.Factory.newInstance(String name, ExpressionExperiment sourceExperiment)	Subsets are named by appending the name to the source experiment name, separated by ExpressionExperimentSubSet.NAME_DELIMITER.
void	ExperimentalDesign.setSecurityOwner(ExpressionExperiment securityOwner)
void	ExperimentalFactor.setSecurityOwner(ExpressionExperiment securityOwner)
void	FactorValue.setSecurityOwner(ExpressionExperiment ee)
void	ExpressionExperimentSubSet.setSourceExperiment(ExpressionExperiment sourceExperiment)

Method parameters in ubic.gemma.model.expression.experiment with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
void	ExpressionExperiment.setOtherParts(Set<ExpressionExperiment> otherParts)

Constructors in ubic.gemma.model.expression.experiment with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	ExpressionExperimentDetailsValueObject(ExpressionExperiment ee)
	ExpressionExperimentDetailsValueObject(ExpressionExperiment ee, boolean skipEvents)	Variant that skips reading the three last*Event associations off CurationDetails when skipEvents=true.
	ExpressionExperimentDetailsValueObject(ExpressionExperiment ee, AclObjectIdentity aoi, AclSid sid)
	ExpressionExperimentValueObject(ExpressionExperiment ee)
	ExpressionExperimentValueObject(ExpressionExperiment ee, boolean ignoreDesign, boolean ignoreAccession)	Creates a new value object out of given Expression Experiment.
	ExpressionExperimentValueObject(ExpressionExperiment ee, boolean ignoreDesign, boolean ignoreAccession, boolean skipEvents)	Variant that skips reading the three last*Event associations off CurationDetails when skipEvents=true.
	ExpressionExperimentValueObject(ExpressionExperiment ee, AclObjectIdentity aoi, AclSid sid)	Creates a new ExpressionExperiment value object with additional information about ownership.

Uses of ExpressionExperiment in ubic.gemma.model.pipeline

Methods in ubic.gemma.model.pipeline that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	PipelineJob.getExperiment()

Methods in ubic.gemma.model.pipeline with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
void	PipelineJob.setExperiment(ExpressionExperiment experiment)

Uses of ExpressionExperiment in ubic.gemma.persistence.persister

Methods in ubic.gemma.persistence.persister that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	EeWriteServiceImpl.create(ExpressionExperiment ee)	No-cache overload: synthesises the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction.
ExpressionExperiment	EeWriteServiceImpl.create(ExpressionExperiment ee, ArrayDesignsForExperimentCache cache)
ExpressionExperiment	PersisterHelper.persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
ExpressionExperiment	PersisterHelperImpl.persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)	Deprecated. use EeWriteService.create(ExpressionExperiment, ArrayDesignsForExperimentCache) directly.

Methods in ubic.gemma.persistence.persister with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	EeWriteServiceImpl.create(ExpressionExperiment ee)	No-cache overload: synthesises the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction.
ExpressionExperiment	EeWriteServiceImpl.create(ExpressionExperiment ee, ArrayDesignsForExperimentCache cache)
ExpressionExperiment	PersisterHelper.persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
ExpressionExperiment	PersisterHelperImpl.persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)	Deprecated. use EeWriteService.create(ExpressionExperiment, ArrayDesignsForExperimentCache) directly.
ArrayDesignsForExperimentCache	PersisterHelper.prepare(ExpressionExperiment ee)
ArrayDesignsForExperimentCache	PersisterHelperImpl.prepare(ExpressionExperiment ee)	Deprecated. use ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) directly.

Uses of ExpressionExperiment in ubic.gemma.persistence.service.analysis.expression

Methods in ubic.gemma.persistence.service.analysis.expression that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	ExpressionExperimentSetDao.getExperimentsInSet(Long id)
Collection<ExpressionExperiment>	ExpressionExperimentSetDaoImpl.getExperimentsInSet(Long id)

Methods in ubic.gemma.persistence.service.analysis.expression with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
Collection<ExpressionExperimentSet>	ExpressionExperimentSetDao.find(ExpressionExperiment ee)
Collection<ExpressionExperimentSet>	ExpressionExperimentSetDaoImpl.find(ExpressionExperiment ee)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.analysis.expression.diff

Methods in ubic.gemma.persistence.service.analysis.expression.diff that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.findByExperimentIds(Collection<Long> experimentIds, boolean includeSubSets, Map<Long, Collection<Long>> arrayDesignUsed, Map<Long, Collection<FactorValue>> ee2fv)	Retrieve analysis for the given experiment or experiment subset IDs.
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)	Find by associated ExpressionExperiments.
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisReadService.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisReadServiceImpl.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)

Methods in ubic.gemma.persistence.service.analysis.expression.diff with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByExperiment(ExpressionExperiment experiment, boolean includeSubSets)	Find by associated ExpressionExperiment.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisReadService.findByExperiment(ExpressionExperiment experimentAnalyzed, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisReadServiceImpl.findByExperiment(ExpressionExperiment experiment, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.findByExperiment(ExpressionExperiment experimentAnalyzed, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByExperiment(ExpressionExperiment experiment, boolean includeSubSets)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisDao.findByExperimentAndAnalysisId(ExpressionExperiment experimentAnalyzed, boolean includeSubSets, Long analysisId)	Find an analysis for the given experiment and identifier.
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisReadService.findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisReadServiceImpl.findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisService.findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisServiceImpl.findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)
void	DifferentialExpressionAnalysisService.removeForExperiment(ExpressionExperiment ee, boolean includeSubSets)	Removes all analyses for the given experiment
void	DifferentialExpressionAnalysisServiceImpl.removeForExperiment(ExpressionExperiment ee, boolean includeSubSets)

Method parameters in ubic.gemma.persistence.service.analysis.expression.diff with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)	Find by associated ExpressionExperiments.
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisReadService.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisReadServiceImpl.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.analysis.expression.pca

Methods in ubic.gemma.persistence.service.analysis.expression.pca with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
PrincipalComponentAnalysis	PrincipalComponentAnalysisService.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)
PrincipalComponentAnalysis	PrincipalComponentAnalysisServiceImpl.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)
boolean	PrincipalComponentAnalysisDao.existsByExperiment(ExpressionExperiment ee)
boolean	PrincipalComponentAnalysisDaoImpl.existsByExperiment(ExpressionExperiment ee)
boolean	PrincipalComponentAnalysisReadService.existsByExperiment(ExpressionExperiment ee)
boolean	PrincipalComponentAnalysisReadServiceImpl.existsByExperiment(ExpressionExperiment ee)
boolean	PrincipalComponentAnalysisService.existsByExperiment(ExpressionExperiment ee)
boolean	PrincipalComponentAnalysisServiceImpl.existsByExperiment(ExpressionExperiment ee)
Collection<PrincipalComponentAnalysis>	PrincipalComponentAnalysisDao.findByExperiment(ExpressionExperiment ee)
Collection<PrincipalComponentAnalysis>	PrincipalComponentAnalysisDaoImpl.findByExperiment(ExpressionExperiment ee)
List<ProbeLoading>	PrincipalComponentAnalysisDao.getTopLoadedProbes(ExpressionExperiment ee, int component, int count)
List<ProbeLoading>	PrincipalComponentAnalysisDaoImpl.getTopLoadedProbes(ExpressionExperiment ee, int component, int count)
List<ProbeLoading>	PrincipalComponentAnalysisReadService.getTopLoadedProbes(ExpressionExperiment ee, int component, int count)
List<ProbeLoading>	PrincipalComponentAnalysisReadServiceImpl.getTopLoadedProbes(ExpressionExperiment ee, int component, int count)
List<ProbeLoading>	PrincipalComponentAnalysisService.getTopLoadedProbes(ExpressionExperiment ee, int component, int count)
List<ProbeLoading>	PrincipalComponentAnalysisServiceImpl.getTopLoadedProbes(ExpressionExperiment ee, int component, int count)
PrincipalComponentAnalysis	PrincipalComponentAnalysisReadService.loadForExperiment(ExpressionExperiment ee)
PrincipalComponentAnalysis	PrincipalComponentAnalysisReadServiceImpl.loadForExperiment(ExpressionExperiment ee)
PrincipalComponentAnalysis	PrincipalComponentAnalysisService.loadForExperiment(ExpressionExperiment ee)
PrincipalComponentAnalysis	PrincipalComponentAnalysisServiceImpl.loadForExperiment(ExpressionExperiment ee)
void	PrincipalComponentAnalysisDao.removeForExperiment(ExpressionExperiment ee)
void	PrincipalComponentAnalysisDaoImpl.removeForExperiment(ExpressionExperiment ee)
void	PrincipalComponentAnalysisService.removeForExperiment(ExpressionExperiment ee)
void	PrincipalComponentAnalysisServiceImpl.removeForExperiment(ExpressionExperiment ee)
PrincipalComponentAnalysis	PrincipalComponentAnalysisService.replaceForExperiment(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)	Remove the experiment's PCA and store the given one, in a single transaction.
PrincipalComponentAnalysis	PrincipalComponentAnalysisServiceImpl.replaceForExperiment(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression

Methods in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)	Computes sample correlation matrices for the given experiment.
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)	Unfortunately, this method breaks under high contention (see #400, so we need to fully lock the database while undergoing using Isolation.SERIALIZABLE transaction isolation level.
boolean	SampleCoexpressionAnalysisService.hasAnalysis(ExpressionExperiment ee)
boolean	SampleCoexpressionAnalysisServiceImpl.hasAnalysis(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.loadBestMatrix(ExpressionExperiment ee)	Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix.
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.loadBestMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.loadFullMatrix(ExpressionExperiment ee)	Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.loadFullMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.loadRegressedMatrix(ExpressionExperiment ee)	Load the regressed coexpression matrix for the given experiment.
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.loadRegressedMatrix(ExpressionExperiment ee)
PreparedCoexMatrices	SampleCoexpressionAnalysisService.prepare(ExpressionExperiment ee)
PreparedCoexMatrices	SampleCoexpressionAnalysisServiceImpl.prepare(ExpressionExperiment ee)	🛑 Propagation.NEVER, and it has to be: this is where the time goes.
void	SampleCoexpressionAuditService.recordSampleCorrelationAnalysis(ExpressionExperiment ee, SampleCorrelationAnalysisPayload payload)	Emit a SampleCorrelationAnalysisEvent for ee, carrying the filter attrition recorded while the matrix was built.
void	SampleCoexpressionAuditServiceImpl.recordSampleCorrelationAnalysis(ExpressionExperiment ee, SampleCorrelationAnalysisPayload payload)
void	SampleCoexpressionAnalysisService.removeForExperiment(ExpressionExperiment ee)	Removes all coexpression matrices for the given experiment.
void	SampleCoexpressionAnalysisServiceImpl.removeForExperiment(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.retrieveExisting(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.retrieveExisting(ExpressionExperiment ee)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.blacklist

Methods in ubic.gemma.persistence.service.blacklist that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	BlacklistedEntityDao.getNonBlacklistedExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	BlacklistedEntityDaoImpl.getNonBlacklistedExpressionExperiments(ArrayDesign arrayDesign)

Methods in ubic.gemma.persistence.service.blacklist with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
BlacklistedExperiment	BlacklistedEntityService.blacklistExpressionExperiment(ExpressionExperiment dataset, String reason)	Blacklist a given dataset.
BlacklistedExperiment	BlacklistedEntityServiceImpl.blacklistExpressionExperiment(ExpressionExperiment dataset, String reason)
boolean	BlacklistedEntityDao.isBlacklisted(ExpressionExperiment dataset)
boolean	BlacklistedEntityDaoImpl.isBlacklisted(ExpressionExperiment dataset)
boolean	BlacklistedEntityService.isBlacklisted(ExpressionExperiment dataset)
boolean	BlacklistedEntityServiceImpl.isBlacklisted(ExpressionExperiment dataset)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.common.description

Methods in ubic.gemma.persistence.service.common.description that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Map<Class<? extends Identifiable>, Map<String, Set<@MayBeUninitialized ExpressionExperiment>>>	CharacteristicDao.findExperimentReferencesByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean rankByLevel)	Similar to CharacteristicDao.findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean), but returns proxies with instead of initializing all the EEs in bulk.
Map<Class<? extends Identifiable>, Map<String, Set<@MayBeUninitialized ExpressionExperiment>>>	CharacteristicDaoImpl.findExperimentReferencesByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean rankByLevel)	Since proxies are returned, they cannot be collected in a HashSet which would otherwise cause their initialization by accessing Object.hashCode().
Map<Class<? extends Identifiable>, Map<String, Set<ExpressionExperiment>>>	CharacteristicDao.findExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean rankByLevel)	This search looks at direct annotations, factor values and biomaterials in that order.
Map<Class<? extends Identifiable>, Map<String, Set<ExpressionExperiment>>>	CharacteristicDaoImpl.findExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean rankByLevel)
Map<Class<? extends Identifiable>, Map<String, Set<ExpressionExperiment>>>	CharacteristicReadService.findExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Class<? extends Identifiable>, Map<String, Set<ExpressionExperiment>>>	CharacteristicReadServiceImpl.findExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Class<? extends Identifiable>, Map<String, Set<ExpressionExperiment>>>	CharacteristicService.findExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Class<? extends Identifiable>, Map<String, Set<ExpressionExperiment>>>	CharacteristicServiceImpl.findExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
LinkedHashMap<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceDao.getRelatedExperiments(Collection<BibliographicReference> records)	Get the related experiments for the given references.
LinkedHashMap<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceDaoImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceReadService.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceReadServiceImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceService.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceServiceImpl.getRelatedExperiments(Collection<BibliographicReference> records)

Methods in ubic.gemma.persistence.service.common.description with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
List<AnnotationRelationDao.RelationSummary>	AnnotationRelationService.findRelationsForExperiment(ExpressionExperiment ee, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, int maxResults)	What this experiment's own annotations imply, for display beside them.
List<AnnotationRelationDao.RelationSummary>	AnnotationRelationServiceImpl.findRelationsForExperiment(ExpressionExperiment ee, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, int maxResults)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.common.quantitationtype

Methods in ubic.gemma.persistence.service.common.quantitationtype with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
QuantitationType	QuantitationTypeDao.find(ExpressionExperiment ee, QuantitationType quantitationType, Set<Class<? extends DataVector>> dataVectorTypes)	Find a QT matching the given template as per QuantitationTypeDao.find(QuantitationType) in a given experiment for and for a given data vector type.
QuantitationType	QuantitationTypeDaoImpl.find(ExpressionExperiment ee, QuantitationType quantitationType, Set<Class<? extends DataVector>> dataVectorTypes)
QuantitationType	QuantitationTypeReadService.find(ExpressionExperiment ee, QuantitationType quantitationType, Class<? extends DataVector> dataVectorTypes)	Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.
QuantitationType	QuantitationTypeReadServiceImpl.find(ExpressionExperiment ee, QuantitationType quantitationType, Class<? extends DataVector> dataVectorTypes)
QuantitationType	QuantitationTypeService.find(ExpressionExperiment ee, QuantitationType quantitationType, Class<? extends DataVector> dataVectorTypes)	Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.
QuantitationType	QuantitationTypeServiceImpl.find(ExpressionExperiment ee, QuantitationType quantitationType, Class<? extends DataVector> dataVectorTypes)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeDao.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeDaoImpl.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeReadService.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeReadServiceImpl.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeService.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)	Find all the QT associated to the given experiment, name and vector type.
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeServiceImpl.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)
Map<Class<? extends DataVector>, Set<QuantitationType>>	QuantitationTypeDao.findByExpressionExperiment(ExpressionExperiment ee)	Retrieve all the QTs associated with the given experiment.
Collection<QuantitationType>	QuantitationTypeDao.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)
Map<Class<? extends DataVector>, Set<QuantitationType>>	QuantitationTypeDaoImpl.findByExpressionExperiment(ExpressionExperiment ee)
Collection<QuantitationType>	QuantitationTypeDaoImpl.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends DataVector> vectorType)
Map<Class<? extends DataVector>, Set<QuantitationType>>	QuantitationTypeReadService.findByExpressionExperiment(ExpressionExperiment ee)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeReadService.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends T> dataVectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeReadService.findByExpressionExperiment(ExpressionExperiment ee, Collection<Class<? extends T>> vectorTypes)	Union of QuantitationTypeReadService.findByExpressionExperiment(ExpressionExperiment, Class) across a collection of vector types.
Map<Class<? extends DataVector>, Set<QuantitationType>>	QuantitationTypeReadServiceImpl.findByExpressionExperiment(ExpressionExperiment ee)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeReadServiceImpl.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends T> dataVectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeReadServiceImpl.findByExpressionExperiment(ExpressionExperiment ee, Collection<Class<? extends T>> vectorTypes)
Map<Class<? extends DataVector>, Set<QuantitationType>>	QuantitationTypeService.findByExpressionExperiment(ExpressionExperiment ee)	Find all the QT associated to the given experiment.
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeService.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends T> dataVectorType)	Find all the QT associated to the given experiment and data vector type.
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeService.findByExpressionExperiment(ExpressionExperiment ee, Collection<Class<? extends T>> vectorTypes)
Map<Class<? extends DataVector>, Set<QuantitationType>>	QuantitationTypeServiceImpl.findByExpressionExperiment(ExpressionExperiment ee)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeServiceImpl.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends T> dataVectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeServiceImpl.findByExpressionExperiment(ExpressionExperiment ee, Collection<Class<? extends T>> vectorTypes)
Collection<QuantitationType>	QuantitationTypeDao.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Retrieve all the QTs associated with the given experiment and dimension.
Collection<QuantitationType>	QuantitationTypeDao.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)	Retrieve all the QTs associated with the given experiment and dimension.
Collection<QuantitationType>	QuantitationTypeDaoImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeDaoImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)
Collection<QuantitationType>	QuantitationTypeReadService.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeReadService.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)
Collection<QuantitationType>	QuantitationTypeReadServiceImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeReadServiceImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)
Collection<QuantitationType>	QuantitationTypeService.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeService.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> dataVectorTypes)
Collection<QuantitationType>	QuantitationTypeServiceImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeServiceImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)
QuantitationType	QuantitationTypeReadService.findByName(ExpressionExperiment ee, String name)	Find a QT by name in a given experiment, defaulting to RawExpressionDataVector.
QuantitationType	QuantitationTypeReadServiceImpl.findByName(ExpressionExperiment ee, String name)
QuantitationType	QuantitationTypeService.findByName(ExpressionExperiment ee, String name)
QuantitationType	QuantitationTypeServiceImpl.findByName(ExpressionExperiment ee, String name)
QuantitationType	QuantitationTypeDao.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)	Find a quantitation type by experiment, name and data vector type.
QuantitationType	QuantitationTypeDaoImpl.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeReadService.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeReadServiceImpl.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeService.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeServiceImpl.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeDao.loadById(Long id, ExpressionExperiment ee)
QuantitationType	QuantitationTypeDaoImpl.loadById(Long id, ExpressionExperiment ee)
QuantitationType	QuantitationTypeReadService.loadById(Long id, ExpressionExperiment ee)
QuantitationType	QuantitationTypeReadServiceImpl.loadById(Long id, ExpressionExperiment ee)
QuantitationType	QuantitationTypeService.loadById(Long value, ExpressionExperiment ee)
QuantitationType	QuantitationTypeServiceImpl.loadById(Long id, ExpressionExperiment ee)
QuantitationType	QuantitationTypeDao.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)	Load a QT from an experiment by ID and vector type.
QuantitationType	QuantitationTypeDaoImpl.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeReadService.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeReadServiceImpl.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeService.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)	Find a quantitation type by ID and vector type.
QuantitationType	QuantitationTypeServiceImpl.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)
List<QuantitationTypeValueObject>	QuantitationTypeDao.loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment ee)	Load QuantitationTypeValueObject in the context of an associated expression experiment.
List<QuantitationTypeValueObject>	QuantitationTypeDaoImpl.loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment ee)
List<QuantitationTypeValueObject>	QuantitationTypeReadService.loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment expressionExperiment)
List<QuantitationTypeValueObject>	QuantitationTypeReadServiceImpl.loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment expressionExperiment)
List<QuantitationTypeValueObject>	QuantitationTypeService.loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment expressionExperiment)
List<QuantitationTypeValueObject>	QuantitationTypeServiceImpl.loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment expressionExperiment)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.expression.arrayDesign

Methods in ubic.gemma.persistence.service.expression.arrayDesign that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	ArrayDesignDao.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignDaoImpl.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignReadService.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignReadServiceImpl.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignService.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignServiceImpl.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignReadService.getSwitchedExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignReadServiceImpl.getSwitchedExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignService.getSwitchedExperiments(ArrayDesign id)	Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.
Collection<ExpressionExperiment>	ArrayDesignServiceImpl.getSwitchedExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignDao.getSwitchedExpressionExperiments(ArrayDesign arrayDesign)	Obtain a collection of ExpressionExperiment identifiers that have been switched from a given platform.
Collection<ExpressionExperiment>	ArrayDesignDaoImpl.getSwitchedExpressionExperiments(ArrayDesign arrayDesign)	Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.

Uses of ExpressionExperiment in ubic.gemma.persistence.service.expression.bioAssay

Methods in ubic.gemma.persistence.service.expression.bioAssay with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
CursorPage<BioAssayValueObject>	BioAssayDao.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)	Cursor-paged listing of BioAssayValueObjects for a single ExpressionExperiment, sorted by ascending id — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
CursorPage<BioAssayValueObject>	BioAssayDaoImpl.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayReadService.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayReadServiceImpl.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayService.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)	Cursor-mode counterpart to the legacy unpaginated BioAssayDao EE-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
CursorPage<BioAssayValueObject>	BioAssayServiceImpl.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.expression.bioAssayData

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Map<ExpressionExperiment, Map<Gene, Collection<Double>>>	ProcessedExpressionDataVectorDao.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment, Map<Gene, Collection<Double>>>	ProcessedExpressionDataVectorDaoImpl.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment, Map<Gene, Collection<Double>>>	ProcessedExpressionDataVectorService.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment, Map<Gene, Collection<Double>>>	ProcessedExpressionDataVectorServiceImpl.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)

Methods in ubic.gemma.persistence.service.expression.bioAssayData with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	ProcessedExpressionDataVectorService.computeUnmaskedProcessedDataMatrix(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)	Rebuild the processed data matrix from raw WITHOUT masking assays flagged as outliers, persisting nothing.
ExpressionDataDoubleMatrix	ProcessedExpressionDataVectorServiceImpl.computeUnmaskedProcessedDataMatrix(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)	🛑 Propagation.NEVER, for the same reason as ProcessedExpressionDataVectorServiceImpl.createProcessedDataVectors(ExpressionExperiment, boolean): the normalization between the read and the assembly is where the 44 minutes go, and nothing in it needs a connection.
QuantitationType	ProcessedExpressionDataVectorService.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks)	Create processed vectors and optionally update ranks.
QuantitationType	ProcessedExpressionDataVectorService.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks, boolean ignoreQuantitationMismatch)	Create processed vectors and optionally update ranks.
QuantitationType	ProcessedExpressionDataVectorServiceImpl.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks)
QuantitationType	ProcessedExpressionDataVectorServiceImpl.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks, boolean ignoreQuantitationMismatch)	🛑 Propagation.NEVER: the quantile normalization in the middle of this takes 44 minutes on a large experiment (GSE260875, measured 2026-09-17) and the connection handling mode is DELAYED_ACQUISITION_AND_HOLD, so a transaction around the whole thing pins a pooled connection for the duration without issuing a statement — against a pool that recycles at 30 minutes.
void	ProcessedExpressionDataVectorService.evictFromCache(ExpressionExperiment ee)
void	ProcessedExpressionDataVectorServiceImpl.evictFromCache(ExpressionExperiment ee)
Collection<T>	AbstractDesignElementDataVectorDao.findByExpressionExperiment(ExpressionExperiment ee)
Collection<T>	DesignElementDataVectorDao.findByExpressionExperiment(ExpressionExperiment ee)
Collection<BulkExpressionDataVector>	RawAndProcessedExpressionDataVectorDaoImpl.findByExpressionExperiment(ExpressionExperiment ee)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArraysByProbe(ExpressionExperiment ee, Collection<CompositeSequence> compositeSequences)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArraysByProbe(ExpressionExperiment ee, Collection<CompositeSequence> compositeSequences)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorService.getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Slice<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorService.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Slice<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorService.getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)	Retrieve and thaw a collection of vectors for a given experiment.
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)
Slice<CompositeSequence>	ProcessedExpressionDataVectorService.getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Slice<CompositeSequence>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDao.getProcessedVectors(ExpressionExperiment expressionExperiment)
List<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDao.getProcessedVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)	Retrieve a slice of processed vectors.
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectors(ExpressionExperiment ee)
List<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectors(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)
List<CompositeSequence>	ProcessedExpressionDataVectorDao.getProcessedVectorsDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)	Only retrieve the design elements for a slice of vectors.
List<CompositeSequence>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectorsDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getRandomProcessedDataArrays(ExpressionExperiment ee, int limit)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getRandomProcessedDataArrays(ExpressionExperiment ee, int limit)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDao.getRandomProcessedVectors(ExpressionExperiment ee, int limit)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDaoImpl.getRandomProcessedVectors(ExpressionExperiment ee, int limit)	Obtain a random sample of processed vectors for the given experiment.
Map<Gene, Collection<Double>>	ProcessedExpressionDataVectorDao.getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene, Collection<Double>>	ProcessedExpressionDataVectorDaoImpl.getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
void	ProcessedExpressionDataVectorAuditService.recordProcessedVectorComputation(ExpressionExperiment ee, ProcessedVectorComputationPayload payload)	Emit a ProcessedVectorComputationEvent for ee with the typed ProcessedVectorComputationPayload.
void	ProcessedExpressionDataVectorAuditServiceImpl.recordProcessedVectorComputation(ExpressionExperiment ee, ProcessedVectorComputationPayload payload)
int	ProcessedExpressionDataVectorService.removeProcessedDataVectors(ExpressionExperiment ee)	Remove the processed vectors of an EE.
int	ProcessedExpressionDataVectorServiceImpl.removeProcessedDataVectors(ExpressionExperiment ee)
void	ProcessedExpressionDataVectorService.reorderByDesign(ExpressionExperiment ee)	Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.
void	ProcessedExpressionDataVectorServiceImpl.reorderByDesign(ExpressionExperiment ee)
int	ProcessedExpressionDataVectorService.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors, boolean updateRanks)	Replace the processed vectors of a EE with the given vectors.
int	ProcessedExpressionDataVectorServiceImpl.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors, boolean updateRanks)
void	ProcessedExpressionDataVectorService.updateRanks(ExpressionExperiment ee)	Update the ranks of the processed vectors for the given experiment.
void	ProcessedExpressionDataVectorServiceImpl.updateRanks(ExpressionExperiment ee)

Method parameters in ubic.gemma.persistence.service.expression.bioAssayData with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
List<ExperimentExpressionLevelsValueObject>	ProcessedExpressionDataVectorService.getExpressionLevels(Collection<ExpressionExperiment> ees, Collection<Gene> genes, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	ProcessedExpressionDataVectorServiceImpl.getExpressionLevels(Collection<ExpressionExperiment> ees, Collection<Gene> genes, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	ProcessedExpressionDataVectorService.getExpressionLevelsDiffEx(Collection<ExpressionExperiment> ees, Long diffExResultSetId, double threshold, int max, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	ProcessedExpressionDataVectorServiceImpl.getExpressionLevelsDiffEx(Collection<ExpressionExperiment> ees, Long diffExResultSetId, double threshold, int max, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	ProcessedExpressionDataVectorService.getExpressionLevelsPca(Collection<ExpressionExperiment> ees, int threshold, int component, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	ProcessedExpressionDataVectorServiceImpl.getExpressionLevelsPca(Collection<ExpressionExperiment> ees, int limit, int component, boolean keepGeneNonSpecific, String consolidateMode)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArrays(Collection<ExpressionExperiment> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(Collection<ExpressionExperiment> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<CompositeSequence> compositeSequences)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<CompositeSequence> compositeSequences)
Map<ProcessedExpressionDataVector, Collection<Long>>	ProcessedExpressionDataVectorDao.getProcessedVectorsAndGenes(Collection<ExpressionExperiment> ees, Map<Long, Collection<Long>> cs2gene)	Obtain processed expression vectors with their associated genes.
Map<ProcessedExpressionDataVector, Collection<Long>>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectorsAndGenes(Collection<ExpressionExperiment> ees, Map<Long, Collection<Long>> cs2gene)
Map<ExpressionExperiment, Map<Gene, Collection<Double>>>	ProcessedExpressionDataVectorDao.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment, Map<Gene, Collection<Double>>>	ProcessedExpressionDataVectorDaoImpl.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment, Map<Gene, Collection<Double>>>	ProcessedExpressionDataVectorService.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment, Map<Gene, Collection<Double>>>	ProcessedExpressionDataVectorServiceImpl.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.expression.biomaterial

Methods in ubic.gemma.persistence.service.expression.biomaterial that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialDao.getExpressionExperiments(BioMaterial bm)	Obtain all the experiments a biomaterial is used in from its hierarchy.
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialDaoImpl.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialReadService.getExpressionExperiments(BioMaterial bm)	Return the ExpressionExperiment occurrences of a given biomaterial, organized by BioAssay.
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialReadServiceImpl.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialService.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialServiceImpl.getExpressionExperiments(BioMaterial bm)

Methods in ubic.gemma.persistence.service.expression.biomaterial with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
Characteristic	BioMaterialService.addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc)	Per-tag add of a characteristic to a biomaterial, the sample-level counterpart of ExpressionExperimentService.addAnnotation(ExpressionExperiment, Characteristic).
Characteristic	BioMaterialService.addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc, String reason)	As BioMaterialService.addAnnotation(ExpressionExperiment, BioMaterial, Characteristic), with a caller-supplied reason appended to the audit note after the server's own description.
Characteristic	BioMaterialServiceImpl.addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc)
Characteristic	BioMaterialServiceImpl.addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc, String reason)	Reason-carrying overload.
Collection<BioMaterial>	BioMaterialDao.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialDaoImpl.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialReadService.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialReadServiceImpl.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialService.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialServiceImpl.findByExperiment(ExpressionExperiment experiment)
Characteristic	BioMaterialService.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId)	Per-tag remove of a characteristic from a biomaterial by id, the sample-level counterpart of ExpressionExperimentService.removeAnnotation(ExpressionExperiment, Long).
Characteristic	BioMaterialService.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId, String reason)	As BioMaterialService.removeAnnotation(ExpressionExperiment, BioMaterial, Long), with a caller-supplied reason appended to the audit note.
Characteristic	BioMaterialServiceImpl.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId)
Characteristic	BioMaterialServiceImpl.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId, String reason)	Reason-carrying overload; see BioMaterialServiceImpl.addAnnotation(ExpressionExperiment, BioMaterial, Characteristic, String).
int	BioMaterialService.updateAnnotations(ExpressionExperiment owner, BioMaterial bm, Collection<Characteristic> desired)	Idempotent set-replace for a biomaterial's direct characteristic set, the sample-level counterpart of ExpressionExperimentService.updateAnnotations(ExpressionExperiment, Collection).
int	BioMaterialServiceImpl.updateAnnotations(ExpressionExperiment owner, BioMaterial bm, Collection<Characteristic> desired)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.expression.experiment

Subclasses with type arguments of type ExpressionExperiment in ubic.gemma.persistence.service.expression.experiment

Modifier and Type	Class	Description
class	ExpressionExperimentDaoImpl
class	ExpressionExperimentServiceImpl

Subinterfaces with type arguments of type ExpressionExperiment in ubic.gemma.persistence.service.expression.experiment

Modifier and Type	Interface	Description
interface	ExpressionExperimentDao	Created by tesarst on 13/03/17.
interface	ExpressionExperimentDao	Created by tesarst on 13/03/17.
interface	ExpressionExperimentDao	Created by tesarst on 13/03/17.
interface	ExpressionExperimentService
interface	ExpressionExperimentService

Methods in ubic.gemma.persistence.service.expression.experiment that return ExpressionExperiment

Modifier and Type	Method	Description
ExpressionExperiment	EeWriteService.create(ExpressionExperiment ee)	Persist an ExpressionExperiment graph, synthesising the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction.
ExpressionExperiment	EeWriteService.create(ExpressionExperiment ee, ArrayDesignsForExperimentCache cache)	Persist an ExpressionExperiment graph.
ExpressionExperiment	ExpressionExperimentDaoImpl.find(ExpressionExperiment entity)
ExpressionExperiment	ExpressionExperimentDao.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentDao.findByBioAssay(BioAssay ba, boolean includeSubSets)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByBioAssay(BioAssay ba, boolean includeSubSets)
ExpressionExperiment	ExpressionExperimentReadService.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentReadService.findByBioAssay(BioAssay ba, boolean includeSubSets)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByBioAssay(BioAssay ba, boolean includeSubSets)
ExpressionExperiment	ExpressionExperimentService.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentService.findByBioAssay(BioAssay ba, boolean includeSubSets)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByBioAssay(BioAssay ba, boolean includeSubSets)
ExpressionExperiment	ExpressionExperimentDao.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentReadService.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentService.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentDao.findByDesignId(Long designId)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByDesignId(Long designId)
ExpressionExperiment	ExpressionExperimentReadService.findByDesignId(Long designId)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByDesignId(Long designId)
ExpressionExperiment	ExpressionExperimentService.findByDesignId(Long designId)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByDesignId(Long designId)
ExpressionExperiment	ExpressionExperimentDao.findByFactor(ExperimentalFactor ef)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactor(ExperimentalFactor ef)
ExpressionExperiment	ExpressionExperimentReadService.findByFactor(ExperimentalFactor factor)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByFactor(ExperimentalFactor factor)
ExpressionExperiment	ExpressionExperimentService.findByFactor(ExperimentalFactor factor)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactor(ExperimentalFactor factor)
ExpressionExperiment	ExpressionExperimentDao.findByFactorValue(FactorValue fv)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactorValue(FactorValue fv)
ExpressionExperiment	ExpressionExperimentReadService.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentService.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentDao.findByFactorValueId(Long factorValueId)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactorValueId(Long factorValueId)
ExpressionExperiment	ExpressionExperimentReadService.findByFactorValueId(Long factorValueId)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByFactorValueId(Long factorValueId)
ExpressionExperiment	ExpressionExperimentService.findByFactorValueId(Long factorValueId)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactorValueId(Long factorValueId)
ExpressionExperiment	ExpressionExperimentDao.findByMeanVarianceRelation(MeanVarianceRelation mvr)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByMeanVarianceRelation(MeanVarianceRelation mvr)
ExpressionExperiment	ExpressionExperimentReadService.findByMeanVarianceRelation(MeanVarianceRelation mvr)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByMeanVarianceRelation(MeanVarianceRelation mvr)
ExpressionExperiment	ExpressionExperimentService.findByMeanVarianceRelation(MeanVarianceRelation mvr)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByMeanVarianceRelation(MeanVarianceRelation mvr)
ExpressionExperiment	ExpressionExperimentDao.findByQuantitationType(QuantitationType quantitationType)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByQuantitationType(QuantitationType quantitationType)
ExpressionExperiment	ExpressionExperimentReadService.findByQuantitationType(QuantitationType type)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByQuantitationType(QuantitationType type)
ExpressionExperiment	ExpressionExperimentService.findByQuantitationType(QuantitationType type)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByQuantitationType(QuantitationType type)
ExpressionExperiment	ExpressionExperimentDao.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentReadService.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentService.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentReadService.findByShortNameAndThawLite(String shortName)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByShortNameAndThawLite(String shortName)
ExpressionExperiment	ExpressionExperimentService.findByShortNameAndThawLite(String shortName)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByShortNameAndThawLite(String shortName)
ExpressionExperiment	ExpressionExperimentReadService.findByShortNameWithPrimaryPublication(String shortName)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByShortNameWithPrimaryPublication(String shortName)
ExpressionExperiment	ExpressionExperimentService.findByShortNameWithPrimaryPublication(String shortName)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByShortNameWithPrimaryPublication(String shortName)
ExpressionExperiment	PreboardedExperimentService.findExpressionExperimentByAccession(String accession)	Look up an existing ExpressionExperiment carrying the given accession.
ExpressionExperiment	PreboardedExperimentServiceImpl.findExpressionExperimentByAccession(String accession)
ExpressionExperiment	ExpressionExperimentDao.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentDaoImpl.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentReadService.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentService.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentServiceImpl.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentDao.findOneByName(String name)
ExpressionExperiment	ExpressionExperimentDaoImpl.findOneByName(String name)
ExpressionExperiment	ExpressionExperimentReadService.findOneByName(String name)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findOneByName(String name)
ExpressionExperiment	ExpressionExperimentService.findOneByName(String name)
ExpressionExperiment	ExpressionExperimentServiceImpl.findOneByName(String name)
ExpressionExperiment	ExpressionExperimentDao.load(Long id, CacheMode cacheMode)	Load an experiment by ID with a specific cache mode.
ExpressionExperiment	ExpressionExperimentDaoImpl.load(Long id, CacheMode cacheMode)
ExpressionExperiment	SingleCellExpressionExperimentService.loadAndInitializeSingleCellDimensions(Long id)	Load an experiment for the single-cell data loader path.
ExpressionExperiment	SingleCellExpressionExperimentServiceImpl.loadAndInitializeSingleCellDimensions(Long id)
ExpressionExperiment	ExpressionExperimentReadService.loadAndThaw(Long id)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadAndThaw(Long id)
ExpressionExperiment	ExpressionExperimentService.loadAndThaw(Long id)	Load an experiment and thaw it as per ExpressionExperimentService.thaw(ExpressionExperiment).
ExpressionExperiment	ExpressionExperimentServiceImpl.loadAndThaw(Long id)
ExpressionExperiment	ExpressionExperimentReadService.loadAndThawLite(Long id)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadAndThawLite(Long id)
ExpressionExperiment	ExpressionExperimentService.loadAndThawLite(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadAndThawLite(Long id)
<T extends Exception> ExpressionExperiment	ExpressionExperimentReadService.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	ExpressionExperimentReadService.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)
<T extends Exception> ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)
<T extends Exception> ExpressionExperiment	ExpressionExperimentService.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	ExpressionExperimentService.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)	Load an experiment and thaw it as per ExpressionExperimentService.thawLite(ExpressionExperiment) or fail with the supplied exception and message.
<T extends Exception> ExpressionExperiment	ExpressionExperimentServiceImpl.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	ExpressionExperimentServiceImpl.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)
<T extends Exception> ExpressionExperiment	ExpressionExperimentReadService.loadAndThawLiterOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadAndThawLiterOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	ExpressionExperimentService.loadAndThawLiterOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	ExpressionExperimentServiceImpl.loadAndThawLiterOrFail(Long id, Function<String,T> exceptionSupplier)
ExpressionExperiment	ExpressionExperimentReadService.loadAndThawLiteWithRefreshCacheMode(Long id)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadAndThawLiteWithRefreshCacheMode(Long id)
ExpressionExperiment	ExpressionExperimentService.loadAndThawLiteWithRefreshCacheMode(Long id)	Load an experiment without cache and thaw it as per ExpressionExperimentService.thaw(ExpressionExperiment) with CacheMode.REFRESH.
ExpressionExperiment	ExpressionExperimentServiceImpl.loadAndThawLiteWithRefreshCacheMode(Long id)
<T extends Exception> ExpressionExperiment	ExpressionExperimentReadService.loadAndThawOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadAndThawOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	ExpressionExperimentService.loadAndThawOrFail(Long id, Function<String,T> exceptionSupplier)	Load an experiment and thaw it as per ExpressionExperimentService.thawLite(ExpressionExperiment) or fail with the supplied exception and message.
<T extends Exception> ExpressionExperiment	ExpressionExperimentServiceImpl.loadAndThawOrFail(Long id, Function<String,T> exceptionSupplier)
ExpressionExperiment	ExpressionExperimentReadService.loadReference(Long id)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadReference(Long id)
ExpressionExperiment	ExpressionExperimentService.loadReference(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadReference(Long id)
ExpressionExperiment	ExpressionExperimentReadService.loadWithAuditTrail(Long id)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadWithAuditTrail(Long id)
ExpressionExperiment	ExpressionExperimentService.loadWithAuditTrail(Long id)	Load an experiment with its audit trail initialized.
ExpressionExperiment	ExpressionExperimentServiceImpl.loadWithAuditTrail(Long id)
ExpressionExperiment	ExpressionExperimentReadService.loadWithCharacteristics(Long id)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadWithCharacteristics(Long id)
ExpressionExperiment	ExpressionExperimentService.loadWithCharacteristics(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadWithCharacteristics(Long id)
ExpressionExperiment	ExpressionExperimentReadService.loadWithMeanVarianceRelation(Long id)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadWithMeanVarianceRelation(Long id)
ExpressionExperiment	ExpressionExperimentService.loadWithMeanVarianceRelation(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadWithMeanVarianceRelation(Long id)
ExpressionExperiment	ExpressionExperimentReadService.loadWithPrimaryPublication(Long id)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadWithPrimaryPublication(Long id)
ExpressionExperiment	ExpressionExperimentService.loadWithPrimaryPublication(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadWithPrimaryPublication(Long id)
ExpressionExperiment	ExpressionExperimentReadService.loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)
ExpressionExperiment	ExpressionExperimentService.loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)
ExpressionExperiment	ExpressionExperimentReadService.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentService.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentServiceImpl.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentReadService.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadService.thawBioAssays(ExpressionExperiment expressionExperiment)	Narrow thaw used by the /samples REST endpoint: initializes only the bioAssays collection and applies Thaws.thawBioAssay(BioAssay) to each assay (which warms the array design, original platform, and biomaterial-with-factor-values shape that BioAssayValueObject reads).
ExpressionExperiment	ExpressionExperimentReadServiceImpl.thawBioAssays(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thawBioAssays(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thawBioAssays(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadService.thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadService.thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thawLiter(ExpressionExperiment expressionExperiment)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
List<ExpressionExperiment>	ExpressionExperimentDaoImpl.browse(int start, int limit)
List<ExpressionExperiment>	ExpressionExperimentDaoImpl.browse(int start, int limit, String orderField, boolean descending)
List<ExpressionExperiment>	ExpressionExperimentReadService.browse(int start, int limit)
List<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.browse(int start, int limit)
List<ExpressionExperiment>	ExpressionExperimentService.browse(int start, int limit)
List<ExpressionExperiment>	ExpressionExperimentServiceImpl.browse(int start, int limit)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByAccession(String accession)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByAccession(String accession)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByAccession(String accession)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByAccession(String accession)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByAccession(String accession)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByAccession(String accession)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentDao.findByBioMaterials(Collection<BioMaterial> bms)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentDaoImpl.findByBioMaterials(Collection<BioMaterial> bms)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentReadService.findByBioMaterials(Collection<BioMaterial> biomaterials)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentReadServiceImpl.findByBioMaterials(Collection<BioMaterial> biomaterials)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentService.findByBioMaterials(Collection<BioMaterial> biomaterials)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentServiceImpl.findByBioMaterials(Collection<BioMaterial> biomaterials)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByExpressedGene(Gene gene, Double rank)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByExpressedGene(Gene gene, Double rank)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByExpressedGene(Gene gene, double rank)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByExpressedGene(Gene gene, double rank)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByExpressedGene(Gene gene, double rank)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByExpressedGene(Gene gene, double rank)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByFactors(Collection<ExperimentalFactor> factors)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByFactors(Collection<ExperimentalFactor> factors)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByFactors(Collection<ExperimentalFactor> factors)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByFactors(Collection<ExperimentalFactor> factors)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByFactors(Collection<ExperimentalFactor> factors)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByFactors(Collection<ExperimentalFactor> factors)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByFactorValueIds(Collection<Long> factorValueIds)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByFactorValueIds(Collection<Long> factorValueIds)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByFactorValueIds(Collection<Long> factorValueIds)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByFactorValueIds(Collection<Long> factorValueIds)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByFactorValueIds(Collection<Long> factorValueIds)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByFactorValueIds(Collection<Long> factorValueIds)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByFactorValues(Collection<FactorValue> fvs)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByFactorValues(Collection<FactorValue> fvs)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByGene(Gene gene)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByGene(Gene gene)	uses GENE2CS table.
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByGene(Gene gene)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByGene(Gene gene)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByGene(Gene gene)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByGene(Gene gene)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByName(String name)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByName(String name)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByName(String name)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByName(String name)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByName(String name)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByName(String name)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByTaxon(Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByTaxon(Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByTaxon(Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByTaxon(Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByTaxon(Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByTaxon(Taxon taxon)
List<ExpressionExperiment>	ExpressionExperimentDao.findByUpdatedLimit(int limit)
List<ExpressionExperiment>	ExpressionExperimentDao.findByUpdatedLimit(Collection<Long> ids, int limit)
List<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByUpdatedLimit(int limit)
List<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByUpdatedLimit(Collection<Long> ids, int limit)
List<ExpressionExperiment>	ExpressionExperimentReadService.findByUpdatedLimit(int limit)
List<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByUpdatedLimit(int limit)
List<ExpressionExperiment>	ExpressionExperimentService.findByUpdatedLimit(int limit)
List<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByUpdatedLimit(int limit)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findUpdatedAfter(Date date)	Find experiments updated on or after a given date.
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findUpdatedAfter(Date date)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findUpdatedAfter(Date date)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findUpdatedAfter(Date date)
Collection<ExpressionExperiment>	ExpressionExperimentService.findUpdatedAfter(Date date)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findUpdatedAfter(Date date)
Map<ExpressionExperiment, Collection<ArrayDesign>>	ExpressionExperimentDao.getArrayDesignsUsedByExperiment(Collection<ExpressionExperiment> ees)	Per-experiment map variant of ExpressionExperimentDao.getArrayDesignsUsed(Collection): one HQL covers all supplied EEs, the result preserves which platform belongs to which EE.
Map<ExpressionExperiment, Collection<ArrayDesign>>	ExpressionExperimentDaoImpl.getArrayDesignsUsedByExperiment(Collection<ExpressionExperiment> ees)
Map<ExpressionExperiment, Collection<ArrayDesign>>	ExpressionExperimentService.getArrayDesignsUsedByExperiment(Collection<ExpressionExperiment> expressionExperiments)	Per-experiment map of array designs used: one HQL covers all supplied EEs and the result preserves which platform belongs to which EE.
Map<ExpressionExperiment, Collection<ArrayDesign>>	ExpressionExperimentServiceImpl.getArrayDesignsUsedByExperiment(Collection<ExpressionExperiment> expressionExperiments)
Collection<ExpressionExperiment>	ExpressionExperimentSetService.getExperimentsInSet(Long id)	Get the (security-filtered) list of experiments in a set.
Collection<ExpressionExperiment>	ExpressionExperimentSetServiceImpl.getExperimentsInSet(Long id)
Collection<ExpressionExperiment>	ExpressionExperimentDao.getExperimentsLackingPublications(int maxResults)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.getExperimentsLackingPublications(int maxResults)
Collection<ExpressionExperiment>	ExpressionExperimentService.getExperimentsLackingPublications(int maxResults)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.getExperimentsLackingPublications(int maxResults)
Collection<ExpressionExperiment>	ExpressionExperimentDao.getExperimentsWithOutliers()
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.getExperimentsWithOutliers()
Collection<ExpressionExperiment>	ExpressionExperimentReadService.getExperimentsWithOutliers()
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.getExperimentsWithOutliers()
Collection<ExpressionExperiment>	ExpressionExperimentService.getExperimentsWithOutliers()
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.getExperimentsWithOutliers()
Map<FactorValue, ExpressionExperiment>	FactorValueDao.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueDaoImpl.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueReadService.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)	Return the ExpressionExperiment that owns each of the given factor values.
Map<FactorValue, ExpressionExperiment>	FactorValueReadServiceImpl.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueService.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)	For efficiency, only the ID, short name and name of the EEs are populated.
Map<FactorValue, ExpressionExperiment>	FactorValueServiceImpl.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<ExpressionExperiment, Collection<BioAssayDimension>>	ExpressionExperimentDao.getProcessedBioAssayDimensions(Collection<ExpressionExperiment> ees)	Batched variant of ExpressionExperimentDao.getProcessedBioAssayDimensions(ExpressionExperiment) — one HQL with an IN clause for the supplied experiments.
Map<ExpressionExperiment, Collection<BioAssayDimension>>	ExpressionExperimentDaoImpl.getProcessedBioAssayDimensions(Collection<ExpressionExperiment> ees)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentDao.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentDaoImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentReadService.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentReadServiceImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentService.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentServiceImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentDao.getSubSetsByExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)	Batched variant of ExpressionExperimentDao.getSubSets(ExpressionExperiment): obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentDaoImpl.getSubSetsByExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)	Batched variant of ExpressionExperimentService.getSubSetsWithBioAssays(ExpressionExperiment): obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadService.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)	Batched variant: obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Taxon>	ExpressionExperimentDao.getTaxa(Collection<ExpressionExperiment> ees)
Map<ExpressionExperiment, Taxon>	ExpressionExperimentDaoImpl.getTaxa(Collection<ExpressionExperiment> ees)
Map<ExpressionExperiment, Taxon>	ExpressionExperimentService.getTaxa(Collection<ExpressionExperiment> ees)	Return the taxon for each of the given experiments.
Map<ExpressionExperiment, Taxon>	ExpressionExperimentServiceImpl.getTaxa(Collection<ExpressionExperiment> ees)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.loadAllReferences()
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.loadAllReferences()
Collection<ExpressionExperiment>	ExpressionExperimentService.loadAllReferences()	Load references for all experiments.
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.loadAllReferences()
Collection<ExpressionExperiment>	ExpressionExperimentDao.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentReadService.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentService.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentDao.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentReadService.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentService.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentReadService.loadReferences(Collection<Long> ids)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.loadReferences(Collection<Long> ids)
Collection<ExpressionExperiment>	ExpressionExperimentService.loadReferences(Collection<Long> ids)	Load references for the given experiment IDs.
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.loadReferences(Collection<Long> ids)
List<ExpressionExperiment>	ExpressionExperimentDao.loadWithCache(Filters filters, Sort sort)
List<ExpressionExperiment>	ExpressionExperimentDao.loadWithRelationsAndCache(List<Long> ids)	Load datasets by IDs with the same relation as ExpressionExperimentDao.loadWithCache(Filters, Sort).
List<ExpressionExperiment>	ExpressionExperimentDaoImpl.loadWithRelationsAndCache(List<Long> ids)

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
Characteristic	ExpressionExperimentService.addAnnotation(ExpressionExperiment ee, Characteristic vc)	Add a single experiment-level tag to ee as part of the per-tag REST write flow.
Characteristic	ExpressionExperimentService.addAnnotation(ExpressionExperiment ee, Characteristic vc, String reason)	As ExpressionExperimentService.addAnnotation(ExpressionExperiment, Characteristic), with a caller-supplied reason appended to the audit note after the server's own description.
Characteristic	ExpressionExperimentServiceImpl.addAnnotation(ExpressionExperiment ee, Characteristic vc)	Per-tag REST-write counterpart to ExpressionExperimentServiceImpl.addCharacteristic(ExpressionExperiment, Characteristic).
Characteristic	ExpressionExperimentServiceImpl.addAnnotation(ExpressionExperiment ee, Characteristic vc, String reason)	Reason-carrying overload.
CellLevelCharacteristics	SingleCellExpressionExperimentService.addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Add new cell-level characteristics.
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)
CellTypeAssignment	SingleCellExpressionExperimentService.addCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, CellTypeAssignment cellTypeAssignment, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.addCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, CellTypeAssignment cta, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)
void	ExpressionExperimentService.addCharacteristic(ExpressionExperiment ee, Characteristic vc)	Will add the vocab characteristic to the expression experiment and persist the changes.
void	ExpressionExperimentServiceImpl.addCharacteristic(ExpressionExperiment ee, Characteristic vc)
void	ExpressionExperimentWriteService.addCharacteristic(ExpressionExperiment ee, Characteristic vc)
void	ExpressionExperimentWriteServiceImpl.addCharacteristic(ExpressionExperiment ee, Characteristic vc)	Will add the characteristic to the expression experiment and persist the changes.
ExperimentalFactor	ExpressionExperimentService.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor	ExpressionExperimentServiceImpl.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor	ExpressionExperimentWriteService.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor	ExpressionExperimentWriteServiceImpl.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
FactorValue	ExpressionExperimentService.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentServiceImpl.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentWriteService.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentWriteServiceImpl.addFactorValue(ExpressionExperiment ee, FactorValue fv)
void	ExpressionExperimentService.addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)	Intended with the case of a continuous factor being added.
void	ExpressionExperimentServiceImpl.addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)
void	ExpressionExperimentWriteService.addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)
void	ExpressionExperimentWriteServiceImpl.addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)
int	ExpressionExperimentDao.addRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> newVectors)	Add raw data vectors with the given quantitation type.
int	ExpressionExperimentDaoImpl.addRawDataVectors(ExpressionExperiment ee, QuantitationType newQt, Collection<RawExpressionDataVector> newVectors)
int	ExpressionExperimentDataVectorService.addRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)	Add raw data vectors for a quantitation type.
int	ExpressionExperimentDataVectorServiceImpl.addRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)
int	ExpressionExperimentService.addRawDataVectors(ExpressionExperiment eeToUpdate, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)	Used when we want to add data for a quantitation type.
int	ExpressionExperimentServiceImpl.addRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)
int	SingleCellExpressionExperimentService.addSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details, boolean recrateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)	Add single-cell data vectors.
int	SingleCellExpressionExperimentService.addSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, SingleCellDimension scd, Stream<SingleCellExpressionDataVector> vectors, String details, boolean recrateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)	Streaming variant of SingleCellExpressionExperimentService.addSingleCellDataVectors(ExpressionExperiment, QuantitationType, Collection, String, boolean, boolean) that avoids materializing all vectors in memory.
int	SingleCellExpressionExperimentServiceImpl.addSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details, boolean recrateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)
int	SingleCellExpressionExperimentServiceImpl.addSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, SingleCellDimension scd, Stream<SingleCellExpressionDataVector> vectors, String details, boolean recrateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)
DesignApplyOutcome	ExpressionExperimentService.applyDesignChange(ExpressionExperiment ee, ExperimentalDesignValueObject proposed)	Apply proposed as the experiment's new ExperimentalDesign.
DesignApplyOutcome	ExpressionExperimentServiceImpl.applyDesignChange(ExpressionExperiment ee, ExperimentalDesignValueObject proposed)
Geeq	GeeqService.calculateScore(ExpressionExperiment ee, GeeqService.ScoreMode mode)	Calculates the GEEQ score in the given mode for the experiment with the given id.
Geeq	GeeqServiceImpl.calculateScore(ExpressionExperiment ee, GeeqService.ScoreMode mode)
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentService.changePreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType quantitationType, CellTypeAssignment newPreferredCta, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentService.changePreferredCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension dimension, CellTypeAssignment newPreferredCta, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)	Change the preferred cell type assignment to the given one.
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentServiceImpl.changePreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType quantitationType, CellTypeAssignment newPreferredCta, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentServiceImpl.changePreferredCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension dimension, CellTypeAssignment newPreferredCta, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentService.clearPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType quantitationType)
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentService.clearPreferredCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension dimension)	Clear the preferred cell type assignment.
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentServiceImpl.clearPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType quantitationType)
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentServiceImpl.clearPreferredCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension dimension)
CurationCommitResult	ExpressionExperimentService.commitCuration(ExpressionExperiment ee, CurationCommitRequest request, boolean dryRun)	Apply an all-or-none curation commit to ee, reconciling the sections carried in request in a single transaction (phase 1: basics + publications).
CurationCommitResult	ExpressionExperimentServiceImpl.commitCuration(ExpressionExperiment ee, CurationCommitRequest request, boolean dryRun)
ExpressionExperiment	EeWriteService.create(ExpressionExperiment ee)	Persist an ExpressionExperiment graph, synthesising the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction.
ExpressionExperiment	EeWriteService.create(ExpressionExperiment ee, ArrayDesignsForExperimentCache cache)	Persist an ExpressionExperiment graph.
ExperimentalFactor	SingleCellExpressionExperimentService.createCellTypeFactor(ExpressionExperiment ee, boolean removeExistingIfNecessary, boolean ignoreCompatibleFactor)	Recreate the cell type factor based on the preferred cell type assignment of the preferred single-cell vectors.
ExperimentalFactor	SingleCellExpressionExperimentServiceImpl.createCellTypeFactor(ExpressionExperiment ee, boolean removeExistingIfNecessary, boolean ignoreCompatibleFactor)
int	ExpressionExperimentDao.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Add processed data vectors
int	ExpressionExperimentDaoImpl.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorService.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorServiceImpl.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentService.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Create a new set of processed vectors for an experiment.
int	ExpressionExperimentServiceImpl.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
void	ExpressionExperimentDao.createSingleCellDataVectors(ExpressionExperiment ee, Iterable<SingleCellExpressionDataVector> vectors)	Create single-cell data vectors in batches to avoid OutOfMemoryError.
void	ExpressionExperimentDaoImpl.createSingleCellDataVectors(ExpressionExperiment ee, Iterable<SingleCellExpressionDataVector> vectors)
void	ExpressionExperimentDao.createSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)	Create a single-cell dimension for a given experiment.
void	ExpressionExperimentDaoImpl.createSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)
void	ExpressionExperimentDao.deleteSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)	Delete the given single-cell dimension.
void	ExpressionExperimentDaoImpl.deleteSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)
protected ExpressionExperimentValueObject	ExpressionExperimentDaoImpl.doLoadValueObject(ExpressionExperiment entity)
void	ExpressionExperimentDao.evictBioAssaysCache(ExpressionExperiment ee)
void	ExpressionExperimentDaoImpl.evictBioAssaysCache(ExpressionExperiment ee)
void	ExpressionExperimentDao.evictCharacteristicsCache(ExpressionExperiment ee)
void	ExpressionExperimentDaoImpl.evictCharacteristicsCache(ExpressionExperiment ee)
void	ExpressionExperimentDao.evictOtherPartsCache(ExpressionExperiment ee)
void	ExpressionExperimentDaoImpl.evictOtherPartsCache(ExpressionExperiment ee)
void	ExpressionExperimentDao.evictQuantitationTypesCache(ExpressionExperiment ee)
void	ExpressionExperimentDaoImpl.evictQuantitationTypesCache(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentDaoImpl.find(ExpressionExperiment entity)
Collection<ExpressionExperimentSet>	ExpressionExperimentSetService.find(ExpressionExperiment ee)
Collection<ExpressionExperimentSet>	ExpressionExperimentSetServiceImpl.find(ExpressionExperiment ee)
List<SingleCellDimensionExperiment>	SingleCellDimensionExperimentDao.findByEE(ExpressionExperiment ee)	All link rows attached to the given EE.
List<SingleCellDimensionExperiment>	SingleCellDimensionExperimentDaoImpl.findByEE(ExpressionExperiment ee)
SingleCellDimensionExperiment	SingleCellDimensionExperimentDao.findByEEAndQt(ExpressionExperiment ee, QuantitationType qt)	Look up the link row for (ee, qt), or null.
SingleCellDimensionExperiment	SingleCellDimensionExperimentDaoImpl.findByEEAndQt(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellDimensionExperimentDao.findDimensionByEEAndQt(ExpressionExperiment ee, QuantitationType qt)	Look up the SingleCellDimension attached to the given (ee, qt) pair via the link table.
SingleCellDimension	SingleCellDimensionExperimentDaoImpl.findDimensionByEEAndQt(ExpressionExperiment ee, QuantitationType qt)
Collection<Long>	ExpressionExperimentSetService.findIds(ExpressionExperiment ee)	security at DAO level
Collection<Long>	ExpressionExperimentSetServiceImpl.findIds(ExpressionExperiment ee)
Map<Class<? extends Identifiable>, List<Characteristic>>	ExpressionExperimentDao.getAllAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)	Obtain all annotations, grouped by applicable level.
Map<Class<? extends Identifiable>, List<Characteristic>>	ExpressionExperimentDaoImpl.getAllAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
Set<AnnotationValueObject>	ExpressionExperimentReadService.getAnnotations(ExpressionExperiment expressionExperiment)
Set<AnnotationValueObject>	ExpressionExperimentReadService.getAnnotations(ExpressionExperiment expressionExperiment, boolean includeFreeText)
Set<AnnotationValueObject>	ExpressionExperimentReadServiceImpl.getAnnotations(ExpressionExperiment expressionExperiment)
Set<AnnotationValueObject>	ExpressionExperimentReadServiceImpl.getAnnotations(ExpressionExperiment expressionExperiment, boolean includeFreeText)
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotations(ExpressionExperiment ee)	Retrieve annotations for a given experiment.
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotations(ExpressionExperiment ee, boolean includeFreeText)	Retrieve annotations for a given experiment, optionally including unmapped ones.
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperiment expressionExperiment)
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperiment expressionExperiment, boolean includeFreeText)
Collection<ArrayDesign>	ExpressionExperimentDao.getArrayDesignsUsed(ExpressionExperiment bas)
Collection<ArrayDesign>	ExpressionExperimentDao.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)
Collection<ArrayDesign>	ExpressionExperimentDaoImpl.getArrayDesignsUsed(ExpressionExperiment bas)
Collection<ArrayDesign>	ExpressionExperimentDaoImpl.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)
Collection<ArrayDesign>	ExpressionExperimentService.getArrayDesignsUsed(ExpressionExperiment expressionExperiment)
Collection<ArrayDesign>	ExpressionExperimentService.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt)	Obtain a collection of ArrayDesign used by a specific set of vectors.
Collection<ArrayDesign>	ExpressionExperimentService.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType)	Obtain a collection of ArrayDesign used by a specific set of vectors.
Collection<ArrayDesign>	ExpressionExperimentServiceImpl.getArrayDesignsUsed(ExpressionExperiment expressionExperiment)
Collection<ArrayDesign>	ExpressionExperimentServiceImpl.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt)
Collection<ArrayDesign>	ExpressionExperimentServiceImpl.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType)
BioAssayDimension	ExpressionExperimentDao.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)	Retrieve a dimension for a given experiment and quantitation type.
BioAssayDimension	ExpressionExperimentDao.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)	Retrieve a dimension for a given experiment and quantitation type.
BioAssayDimension	ExpressionExperimentDaoImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)
BioAssayDimension	ExpressionExperimentDaoImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentService.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)	Obtain the dimension associated to the given quantitation type for the given experiment.
BioAssayDimension	ExpressionExperimentService.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentDao.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)	Obtain a bioassay dimension by ID.
BioAssayDimension	ExpressionExperimentDaoImpl.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentService.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId)	Find a BioAssayDimension by ID.
BioAssayDimension	ExpressionExperimentService.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<BioAssayDimension>	ExpressionExperimentDao.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentDao.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt)
Collection<BioAssayDimension>	ExpressionExperimentDao.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<BioAssayDimension>	ExpressionExperimentService.getBioAssayDimensionsWithAssays(ExpressionExperiment expressionExperiment)	Obtain all the dimensions associated to the given experiment.
Collection<BioAssayDimension>	ExpressionExperimentService.getBioAssayDimensionsWithAssays(ExpressionExperiment ee, QuantitationType qt)	Obtain all BioAssayDimensions associated to a particular QuantitationType.
Collection<BioAssayDimension>	ExpressionExperimentServiceImpl.getBioAssayDimensionsWithAssays(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentServiceImpl.getBioAssayDimensionsWithAssays(ExpressionExperiment ee, QuantitationType qt)
List<Characteristic>	ExpressionExperimentDao.getBioMaterialAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)	Obtain sample-level annotations.
List<Characteristic>	ExpressionExperimentDaoImpl.getBioMaterialAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
long	ExpressionExperimentDao.getBioMaterialCount(ExpressionExperiment expressionExperiment)
long	ExpressionExperimentDaoImpl.getBioMaterialCount(ExpressionExperiment expressionExperiment)
long	ExpressionExperimentReadService.getBioMaterialCount(ExpressionExperiment expressionExperiment)
long	ExpressionExperimentReadServiceImpl.getBioMaterialCount(ExpressionExperiment expressionExperiment)
long	ExpressionExperimentService.getBioMaterialCount(ExpressionExperiment expressionExperiment)
long	ExpressionExperimentServiceImpl.getBioMaterialCount(ExpressionExperiment expressionExperiment)
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee)	Obtain all cell-level characteristics from all single-cell dimensions.
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain all cell-level characteristics from all single-cell dimensions matching the given category.
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
CellLevelCharacteristics	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, Long clcId)	Obtain a specific cell-level characteristic by ID.
CellLevelCharacteristics	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String clcName)
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Category category)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
CellLevelCharacteristics	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String clcName)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Category category)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain CLC for given category.
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
CellLevelCharacteristics	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Long id)
CellLevelCharacteristics	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String name)	Obtain a CLC by name.
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Long id)
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String name)
Category	SingleCellExpressionExperimentService.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
Category	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
Collection<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellLevelCharacteristics	ExpressionExperimentDao.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	ExpressionExperimentDao.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
Collection<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellLevelCharacteristics	ExpressionExperimentDaoImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	ExpressionExperimentDaoImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
Collection<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellLevelCharacteristics	SingleCellExpressionExperimentService.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long ctaId)
CellLevelCharacteristics	SingleCellExpressionExperimentService.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
Collection<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
Optional<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelMask(ExpressionExperiment expressionExperiment, QuantitationType qt)	Obtain a mask if one is unambiguously defined for the given experiment and quantitation type.
Optional<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelMask(ExpressionExperiment expressionExperiment, QuantitationType qt)
CellTypeAssignment	ExpressionExperimentDao.getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)	Obtain a cell type assignment by ID.
CellTypeAssignment	ExpressionExperimentDao.getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)	Obtain a cell type assignment by name.
CellTypeAssignment	ExpressionExperimentDaoImpl.getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)
CellTypeAssignment	ExpressionExperimentDaoImpl.getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)
CellTypeAssignment	SingleCellExpressionExperimentService.getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)	Obtain a cell type assignment by ID.
CellTypeAssignment	SingleCellExpressionExperimentService.getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)	Obtain a cell type assignment by name.
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)
Collection<CellTypeAssignment>	ExpressionExperimentDao.getCellTypeAssignmentByProtocol(ExpressionExperiment ee, QuantitationType qt, String protocolIdentifier)
Collection<CellTypeAssignment>	ExpressionExperimentDaoImpl.getCellTypeAssignmentByProtocol(ExpressionExperiment ee, QuantitationType qt, String protocolName)
Collection<CellTypeAssignment>	SingleCellExpressionExperimentService.getCellTypeAssignmentByProtocol(ExpressionExperiment ee, QuantitationType qt, String protocolName)	Obtain a cell type assignment by a protocol identifier.
Collection<CellTypeAssignment>	SingleCellExpressionExperimentServiceImpl.getCellTypeAssignmentByProtocol(ExpressionExperiment ee, QuantitationType qt, String protocolName)
List<CellTypeAssignment>	ExpressionExperimentDao.getCellTypeAssignments(ExpressionExperiment ee)
List<CellTypeAssignment>	ExpressionExperimentDao.getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)
List<CellTypeAssignment>	ExpressionExperimentDaoImpl.getCellTypeAssignments(ExpressionExperiment ee)
List<CellTypeAssignment>	ExpressionExperimentDaoImpl.getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)
List<CellTypeAssignment>	SingleCellExpressionExperimentService.getCellTypeAssignments(ExpressionExperiment ee)	Obtain all the cell type labellings from all single-cell vectors.
List<CellTypeAssignment>	SingleCellExpressionExperimentService.getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)
List<CellTypeAssignment>	SingleCellExpressionExperimentServiceImpl.getCellTypeAssignments(ExpressionExperiment ee)
List<CellTypeAssignment>	SingleCellExpressionExperimentServiceImpl.getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)
Collection<CellTypeAssignment>	ExpressionExperimentDao.getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Collection<CellTypeAssignment>	ExpressionExperimentDaoImpl.getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Collection<CellTypeAssignment>	SingleCellExpressionExperimentService.getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Collection<CellTypeAssignment>	SingleCellExpressionExperimentServiceImpl.getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellTypeAssignment	ExpressionExperimentDao.getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)	Obtain a cell type assignment by ID without loading the indices.
CellTypeAssignment	ExpressionExperimentDao.getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)	Obtain a cell type assignment by name without loading the indices.
CellTypeAssignment	ExpressionExperimentDaoImpl.getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)
CellTypeAssignment	ExpressionExperimentDaoImpl.getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)
CellTypeAssignment	SingleCellExpressionExperimentService.getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long ctaId)
CellTypeAssignment	SingleCellExpressionExperimentService.getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String ctaName)
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long ctaId)
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String ctaName)
Characteristic	SingleCellExpressionExperimentService.getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, Long ctaId, int cellIndex)
Characteristic[]	SingleCellExpressionExperimentService.getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, Long ctaId, int startIndex, int endIndexExclusive)
Characteristic	SingleCellExpressionExperimentService.getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, String ctaName, int cellIndex)
Characteristic[]	SingleCellExpressionExperimentService.getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, String ctaName, int startIndex, int endIndexExclusive)
Characteristic	SingleCellExpressionExperimentServiceImpl.getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, Long ctaId, int cellIndex)
Characteristic[]	SingleCellExpressionExperimentServiceImpl.getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, Long ctaId, int startIndex, int endIndexExclusive)
Characteristic	SingleCellExpressionExperimentServiceImpl.getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, String ctaName, int cellIndex)
Characteristic[]	SingleCellExpressionExperimentServiceImpl.getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, String ctaName, int startIndex, int endIndexExclusive)
Optional<ExperimentalFactor>	SingleCellExpressionExperimentService.getCellTypeFactor(ExpressionExperiment ee)	Obtain the cell type factor.
Optional<ExperimentalFactor>	SingleCellExpressionExperimentServiceImpl.getCellTypeFactor(ExpressionExperiment ee)
List<Characteristic>	ExpressionExperimentDao.getCellTypes(ExpressionExperiment ee)
List<Characteristic>	ExpressionExperimentDaoImpl.getCellTypes(ExpressionExperiment ee)
List<Characteristic>	SingleCellExpressionExperimentService.getCellTypes(ExpressionExperiment ee)	Obtain the cell types of a given single-cell dataset.
List<Characteristic>	SingleCellExpressionExperimentServiceImpl.getCellTypes(ExpressionExperiment ee)
String	ExpressionExperimentMetaFileType.getDownloadName(ExpressionExperiment ee)
List<Characteristic>	ExpressionExperimentDao.getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)	Obtain experimental design-level annotations.
List<Characteristic>	ExpressionExperimentDaoImpl.getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
ExperimentalDesignValueObject	ExpressionExperimentReadService.getExperimentalDesignValueObject(ExpressionExperiment ee)
ExperimentalDesignValueObject	ExpressionExperimentReadServiceImpl.getExperimentalDesignValueObject(ExpressionExperiment ee)
ExperimentalDesignValueObject	ExpressionExperimentService.getExperimentalDesignValueObject(ExpressionExperiment ee)	Build a full structured representation of an experiment's ExperimentalDesign: factors, factor values (with statements carrying stable database IDs), and per-biomaterial factor-value assignments.
ExperimentalDesignValueObject	ExpressionExperimentServiceImpl.getExperimentalDesignValueObject(ExpressionExperiment ee)
Collection<Characteristic>	ExpressionExperimentDao.getExperimentAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)	Obtain experiment-level annotations.
List<Characteristic>	ExpressionExperimentDaoImpl.getExperimentAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
Collection<Characteristic>	ExpressionExperimentDao.getExperimentSubSetAnnotations(ExpressionExperiment ee)	Obtain the subset annotations.
Collection<Characteristic>	ExpressionExperimentDaoImpl.getExperimentSubSetAnnotations(ExpressionExperiment ee)
List<Statement>	ExpressionExperimentDao.getFactorValueAnnotations(ExpressionExperiment ee)	Obtain factor value-level annotations.
List<Statement>	ExpressionExperimentDaoImpl.getFactorValueAnnotations(ExpressionExperiment ee)
List<Object[]>	ExpressionExperimentDao.getFactorValueAnnotationsWithParents(ExpressionExperiment ee)	Obtain factor value-level annotations together with the owning factor value and experimental factor, so the read VO can carry the term's parent context (parentName = the factor value, parentOfParentName = the factor) without a second query.
List<Object[]>	ExpressionExperimentDaoImpl.getFactorValueAnnotationsWithParents(ExpressionExperiment ee)
String	ExpressionExperimentMetaFileType.getFileName(ExpressionExperiment ee)
Collection<Gene>	ExpressionExperimentDao.getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)	Obtain genes used by the processed vectors of this dataset.
Collection<Gene>	ExpressionExperimentDaoImpl.getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)
Collection<Gene>	ExpressionExperimentService.getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)	Retrieve the genes used by the preferred vectors of this experiment.
Collection<Gene>	ExpressionExperimentServiceImpl.getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)
GeoSeries	ExpressionExperimentGeoService.getGeoSeries(ExpressionExperiment ee)	Obtain the GEO series metadata.
GeoSeries	ExpressionExperimentGeoServiceImpl.getGeoSeries(ExpressionExperiment ee)
Date	ExpressionExperimentDao.getLastArrayDesignUpdate(ExpressionExperiment ee)
Date	ExpressionExperimentDaoImpl.getLastArrayDesignUpdate(ExpressionExperiment ee)
Date	ExpressionExperimentReadService.getLastArrayDesignUpdate(ExpressionExperiment ee)
Date	ExpressionExperimentReadServiceImpl.getLastArrayDesignUpdate(ExpressionExperiment ee)
Date	ExpressionExperimentService.getLastArrayDesignUpdate(ExpressionExperiment expressionExperiment)
Date	ExpressionExperimentServiceImpl.getLastArrayDesignUpdate(ExpressionExperiment ee)
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentDao.getMissingValuesVectors(ExpressionExperiment ee)	Obtain the missing value vectors for a given experiment.
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentDaoImpl.getMissingValuesVectors(ExpressionExperiment ee)
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentDataVectorService.getMissingValuesVectors(ExpressionExperiment ee)
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentDataVectorServiceImpl.getMissingValuesVectors(ExpressionExperiment ee)
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentService.getMissingValuesVectors(ExpressionExperiment ee)
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentServiceImpl.getMissingValuesVectors(ExpressionExperiment ee)
Map<BioAssay,Long>	ExpressionExperimentDao.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<BioAssay,Long>	ExpressionExperimentDaoImpl.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<BioAssay,Long>	ExpressionExperimentReadService.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<BioAssay,Long>	ExpressionExperimentReadServiceImpl.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<BioAssay,Long>	ExpressionExperimentService.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)	Obtain the number of design elements for the platform of each bioassay in the given experiment.
Map<BioAssay,Long>	ExpressionExperimentServiceImpl.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
long	ExpressionExperimentDao.getNumberOfNonZeroes(ExpressionExperiment ee, QuantitationType qt)	Obtain the number of non-zeroes.
long	ExpressionExperimentDaoImpl.getNumberOfNonZeroes(ExpressionExperiment ee, QuantitationType qt)
long	SingleCellExpressionExperimentService.getNumberOfNonZeroes(ExpressionExperiment ee, QuantitationType qt)
long	SingleCellExpressionExperimentServiceImpl.getNumberOfNonZeroes(ExpressionExperiment ee, QuantitationType qt)
Map<BioAssay,Long>	ExpressionExperimentDao.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)	Obtain the number of non-zeroes by sample.
Map<BioAssay,Long>	ExpressionExperimentDaoImpl.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)
Map<BioAssay,Long>	SingleCellExpressionExperimentService.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)
Map<BioAssay,Long>	SingleCellExpressionExperimentServiceImpl.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)
long	ExpressionExperimentDao.getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)	Obtain the number of single-cell vectors for a given QT.
long	ExpressionExperimentDao.getNumberOfSingleCellDataVectors(ExpressionExperiment ee, SingleCellDimension scd)	Obtain the number of single-cell vectors for a given single-cell dimension.
long	ExpressionExperimentDaoImpl.getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)
long	ExpressionExperimentDaoImpl.getNumberOfSingleCellDataVectors(ExpressionExperiment ee, SingleCellDimension scd)
long	SingleCellExpressionExperimentService.getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)	Obtain the number of single-cell vectors for a given quantitation type.
long	SingleCellExpressionExperimentServiceImpl.getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)
CellTypeAssignment	ExpressionExperimentDao.getPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt)	Obtain the preferred assignment for the given quantitation type.
CellTypeAssignment	ExpressionExperimentDaoImpl.getPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt)
Optional<CellTypeAssignment>	SingleCellExpressionExperimentService.getPreferredCellTypeAssignment(ExpressionExperiment ee)	Obtain the preferred cell type labelling from the preferred single-cell vectors.
Optional<CellTypeAssignment>	SingleCellExpressionExperimentService.getPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt)
Optional<CellTypeAssignment>	SingleCellExpressionExperimentServiceImpl.getPreferredCellTypeAssignment(ExpressionExperiment ee)
Optional<CellTypeAssignment>	SingleCellExpressionExperimentServiceImpl.getPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt)
CellTypeAssignment	ExpressionExperimentDao.getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt)	Obtain the preferred assignment for the given quantitation type without loading the indices.
CellTypeAssignment	ExpressionExperimentDaoImpl.getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Optional<CellTypeAssignment>	SingleCellExpressionExperimentService.getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee)
Optional<CellTypeAssignment>	SingleCellExpressionExperimentService.getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Optional<CellTypeAssignment>	SingleCellExpressionExperimentServiceImpl.getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee)
Optional<CellTypeAssignment>	SingleCellExpressionExperimentServiceImpl.getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
QuantitationType	ExpressionExperimentDao.getPreferredQuantitationType(ExpressionExperiment ee)	Obtain the preferred quantitation type for the raw vectors, if available.
QuantitationType	ExpressionExperimentDaoImpl.getPreferredQuantitationType(ExpressionExperiment ee)
Optional<QuantitationType>	ExpressionExperimentService.getPreferredQuantitationType(ExpressionExperiment ee)	Iterates over the quantitation types for a given expression experiment and returns the preferred quantitation types.
Optional<QuantitationType>	ExpressionExperimentServiceImpl.getPreferredQuantitationType(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	ExpressionExperimentDao.getPreferredRawDataVectors(ExpressionExperiment ee)	Obtain the preferred raw data vectors for a given experiment.
Collection<RawExpressionDataVector>	ExpressionExperimentDaoImpl.getPreferredRawDataVectors(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorService.getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorServiceImpl.getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Collection<RawExpressionDataVector>	ExpressionExperimentService.getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Collection<RawExpressionDataVector>	ExpressionExperimentServiceImpl.getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Optional<Collection<SingleCellExpressionDataVector>>	SingleCellExpressionExperimentService.getPreferredSingleCellDataVectors(ExpressionExperiment ee)	Obtain preferred single-cell vectors.
Optional<Collection<SingleCellExpressionDataVector>>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDataVectors(ExpressionExperiment ee)
SingleCellDimension	ExpressionExperimentDao.getPreferredSingleCellDimension(ExpressionExperiment ee)	Obtain the preferred single-cell dimension, that is the dimension associated to the preferred set of single-cell vectors.
SingleCellDimension	ExpressionExperimentDaoImpl.getPreferredSingleCellDimension(ExpressionExperiment ee)
Optional<SingleCellDimension>	SingleCellExpressionExperimentService.getPreferredSingleCellDimension(ExpressionExperiment ee)	Obtain the preferred single-cell dimension.
Optional<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDimension(ExpressionExperiment ee)
SingleCellDimension	ExpressionExperimentDao.getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	ExpressionExperimentDaoImpl.getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
Optional<SingleCellDimension>	SingleCellExpressionExperimentService.getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee)	Obtain the preferred single-cell dimension.
Optional<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee)
SingleCellDimension	ExpressionExperimentDao.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)	Load a single-cell dimension without its cell IDs.
SingleCellDimension	ExpressionExperimentDaoImpl.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)
Optional<SingleCellDimension>	SingleCellExpressionExperimentService.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)	Obtain the preferred single-cell dimension without its cell IDs.
Optional<SingleCellDimension>	SingleCellExpressionExperimentService.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)
Optional<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)
Optional<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
QuantitationType	ExpressionExperimentDao.getPreferredSingleCellQuantitationType(ExpressionExperiment ee)	Obtain the preferred quantitation type for single-cell data, if available.
QuantitationType	ExpressionExperimentDaoImpl.getPreferredSingleCellQuantitationType(ExpressionExperiment ee)
Optional<QuantitationType>	SingleCellExpressionExperimentService.getPreferredSingleCellQuantitationType(ExpressionExperiment ee)	Obtain the preferred single-cell quantitation type.
Optional<QuantitationType>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellQuantitationType(ExpressionExperiment ee)
BioAssayDimension	ExpressionExperimentDao.getProcessedBioAssayDimension(ExpressionExperiment ee)	Retrieve the dimension associated to the procesed data vectors.
BioAssayDimension	ExpressionExperimentDaoImpl.getProcessedBioAssayDimension(ExpressionExperiment ee)
BioAssayDimension	ExpressionExperimentService.getProcessedBioAssayDimension(ExpressionExperiment ee)	Obtain the dimension associated to the processed data for the given experiment.
BioAssayDimension	ExpressionExperimentServiceImpl.getProcessedBioAssayDimension(ExpressionExperiment ee)
Collection<BioAssayDimension>	ExpressionExperimentDao.getProcessedBioAssayDimensions(ExpressionExperiment ee)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getProcessedBioAssayDimensions(ExpressionExperiment ee)
Collection<BioAssayDimension>	ExpressionExperimentService.getProcessedBioAssayDimensionsWithAssays(ExpressionExperiment ee)	Obtain the dimension associated to the processed data for the given experiment.
Collection<BioAssayDimension>	ExpressionExperimentServiceImpl.getProcessedBioAssayDimensionsWithAssays(ExpressionExperiment ee)
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment ee)	Retrieve the processed vector for an experiment.
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)	Retrieve a slice of processed vectors for an experiment.
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDaoImpl.getProcessedDataVectors(ExpressionExperiment ee)
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDaoImpl.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentDataVectorService.getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentDataVectorService.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentService.getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentService.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentServiceImpl.getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentServiceImpl.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
QuantitationType	ExpressionExperimentDao.getProcessedQuantitationType(ExpressionExperiment ee)	Obtain the quantitation type for the processed vectors, if available.
QuantitationType	ExpressionExperimentDaoImpl.getProcessedQuantitationType(ExpressionExperiment ee)
Optional<QuantitationType>	ExpressionExperimentService.getProcessedQuantitationType(ExpressionExperiment ee)
Optional<QuantitationType>	ExpressionExperimentServiceImpl.getProcessedQuantitationType(ExpressionExperiment ee)
Map<QuantitationType, Long>	ExpressionExperimentDao.getQuantitationTypeCount(ExpressionExperiment ee)
Map<QuantitationType, Long>	ExpressionExperimentDaoImpl.getQuantitationTypeCount(ExpressionExperiment ee)
Map<QuantitationType, Long>	ExpressionExperimentService.getQuantitationTypeCount(ExpressionExperiment ee)
Map<QuantitationType, Long>	ExpressionExperimentServiceImpl.getQuantitationTypeCount(ExpressionExperiment ee)
Collection<QuantitationType>	ExpressionExperimentService.getQuantitationTypes(ExpressionExperiment expressionExperiment)	Retrieve all the quantitation types used by the given expression experiment.
Collection<QuantitationType>	ExpressionExperimentService.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Retrieve all the quantitation types used by the given experiment and dimension.
Collection<QuantitationType>	ExpressionExperimentService.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<QuantitationType>	ExpressionExperimentServiceImpl.getQuantitationTypes(ExpressionExperiment expressionExperiment)
Collection<QuantitationType>	ExpressionExperimentServiceImpl.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	ExpressionExperimentServiceImpl.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Class<? extends BulkExpressionDataVector> dataVectorType)
Map<Class<? extends DataVector>, Set<QuantitationType>>	ExpressionExperimentService.getQuantitationTypesByVectorType(ExpressionExperiment ee)
Map<Class<? extends DataVector>, Set<QuantitationType>>	ExpressionExperimentServiceImpl.getQuantitationTypesByVectorType(ExpressionExperiment ee)
Collection<QuantitationTypeValueObject>	ExpressionExperimentService.getQuantitationTypeValueObjects(ExpressionExperiment expressionExperiment)	Load all QuantitationType associated to an expression experiment as VOs.
Collection<QuantitationTypeValueObject>	ExpressionExperimentServiceImpl.getQuantitationTypeValueObjects(ExpressionExperiment expressionExperiment)
long	ExpressionExperimentDao.getRawDataVectorCount(ExpressionExperiment ee)
long	ExpressionExperimentDao.getRawDataVectorCount(ExpressionExperiment ee, QuantitationType qt)
long	ExpressionExperimentDaoImpl.getRawDataVectorCount(ExpressionExperiment ee)
long	ExpressionExperimentDaoImpl.getRawDataVectorCount(ExpressionExperiment ee, QuantitationType quantitationType)
long	ExpressionExperimentReadService.getRawDataVectorCount(ExpressionExperiment ee)
long	ExpressionExperimentReadServiceImpl.getRawDataVectorCount(ExpressionExperiment ee)
long	ExpressionExperimentService.getRawDataVectorCount(ExpressionExperiment ee)
long	ExpressionExperimentServiceImpl.getRawDataVectorCount(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType qt)	Obtain a slice of the raw vectors for a given experiment and QT.
Collection<RawExpressionDataVector>	ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)	Obtain raw vectors for a given experiment and QT.
Collection<RawExpressionDataVector>	ExpressionExperimentDaoImpl.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDaoImpl.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorService.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorService.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorServiceImpl.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorServiceImpl.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentService.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentService.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentServiceImpl.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentServiceImpl.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
List<SingleCellExpressionDataVector>	ExpressionExperimentDao.getSingleCellDataVectors(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)	Obtain a set of single-cell data vectors for the given quantitation type.
List<SingleCellExpressionDataVector>	ExpressionExperimentDao.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean includeBiologicalCharacteristics, boolean includeCellIds, boolean includeData, boolean includeDataIndices)	Obtain a set of single-cell data vectors for the given quantitation type.
List<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.getSingleCellDataVectors(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)
List<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean includeBiologicalCharacteristics, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)	Obtain single-cell vectors for a particular sample.
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain single-cell vectors for a given quantitation type.
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
List<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
SingleCellExpressionDataVector	ExpressionExperimentDao.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)
SingleCellExpressionDataVector	ExpressionExperimentDaoImpl.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)
SingleCellExpressionDataVector	SingleCellExpressionExperimentService.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)	Obtain a single single-cell vector without initializing cell IDs.
SingleCellExpressionDataVector	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimension(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain the single-cell dimension used by a specific QT.
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)	Obtain a single-cell dimension used for a given dataset and QT.
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimensionById(ExpressionExperiment expressionExperiment, Long id)	Obtain a single-cell dimension by ID.
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionById(ExpressionExperiment expressionExperiment, Long dimensionId)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionByIdWithoutCellIds(ExpressionExperiment expressionExperiment, Long id, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionByIdWithoutCellIds(ExpressionExperiment expressionExperiment, Long dimensionId, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimensionForCellLevelCharacteristicsById(ExpressionExperiment ee, Long clcId)
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionForCellLevelCharacteristicsById(ExpressionExperiment ee, Long clcId)
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimensionForCellTypeAssignmentById(ExpressionExperiment ee, Long ctaId)
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionForCellTypeAssignmentById(ExpressionExperiment ee, Long ctaId)
List<SingleCellDimension>	ExpressionExperimentDao.getSingleCellDimensions(ExpressionExperiment ee)	Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.
List<SingleCellDimension>	ExpressionExperimentDaoImpl.getSingleCellDimensions(ExpressionExperiment ee)
List<SingleCellDimension>	SingleCellExpressionExperimentService.getSingleCellDimensions(ExpressionExperiment ee)	Obtain all the single-cell dimensions used by a given dataset.
List<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensions(ExpressionExperiment ee)
List<SingleCellDimension>	ExpressionExperimentDao.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)	Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.
List<SingleCellDimension>	ExpressionExperimentDao.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
List<SingleCellDimension>	ExpressionExperimentDaoImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	ExpressionExperimentDaoImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
List<SingleCellDimension>	SingleCellExpressionExperimentService.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	SingleCellExpressionExperimentService.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)
List<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)	Retrieve a single-cell dimension with its bioassays and cell-level characteristics initialized.
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)	Load a single-cell dimension used by a specific QT without its cell IDs.
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimensionWithoutCellIdsById(ExpressionExperiment expressionExperiment, Long dimensionId, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionWithoutCellIdsById(ExpressionExperiment expressionExperiment, Long dimensionId, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentService.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, List<BioAssay> samples, QuantitationType quantitationType)	Obtain a single-cell expression data matrix for the given quantitation type.
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentService.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)	Obtain a single-cell expression data matrix for the given quantitation type.
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentServiceImpl.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, List<BioAssay> samples, QuantitationType quantitationType)
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentServiceImpl.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)
List<QuantitationType>	ExpressionExperimentDao.getSingleCellQuantitationTypes(ExpressionExperiment ee)	Obtain a list of single-cell QTs.
List<QuantitationType>	ExpressionExperimentDaoImpl.getSingleCellQuantitationTypes(ExpressionExperiment ee)
Collection<QuantitationType>	SingleCellExpressionExperimentService.getSingleCellQuantitationTypes(ExpressionExperiment ee)
Collection<QuantitationType>	SingleCellExpressionExperimentServiceImpl.getSingleCellQuantitationTypes(ExpressionExperiment ee)
Map<SingleCellDimension, Set<QuantitationType>>	ExpressionExperimentDao.getSingleCellQuantitationTypesBySingleCellDimensionWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
Map<SingleCellDimension, Set<QuantitationType>>	ExpressionExperimentDaoImpl.getSingleCellQuantitationTypesBySingleCellDimensionWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
Map<SingleCellDimension, Set<QuantitationType>>	SingleCellExpressionExperimentService.getSingleCellQuantitationTypesBySingleCellDimensionWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)	Obtain the single-cell quantitation types by single-cell dimension.
Map<SingleCellDimension, Set<QuantitationType>>	SingleCellExpressionExperimentServiceImpl.getSingleCellQuantitationTypesBySingleCellDimensionWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
String	ExpressionExperimentDao.getSourceMetadata(ExpressionExperiment ee)	The stored GEO source metadata document, or null when none has been harvested.
String	ExpressionExperimentDaoImpl.getSourceMetadata(ExpressionExperiment ee)
String	ExpressionExperimentService.getSourceMetadata(ExpressionExperiment ee)
String	ExpressionExperimentServiceImpl.getSourceMetadata(ExpressionExperiment ee)
ExpressionExperimentSubSet	ExpressionExperimentDao.getSubSetById(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentDaoImpl.getSubSetById(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentService.getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentServiceImpl.getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadService.getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID, with characteristics initialized.
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadServiceImpl.getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentService.getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID.
ExpressionExperimentSubSet	ExpressionExperimentServiceImpl.getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadService.getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID, with characteristics initialized and assays thawed.
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadServiceImpl.getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDao.getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDao.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension bad)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDaoImpl.getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDaoImpl.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension bad)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentDao.getSubSetsByDimension(ExpressionExperiment expressionExperiment)
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentDaoImpl.getSubSetsByDimension(ExpressionExperiment expressionExperiment)
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsByDimension(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsByDimension(ExpressionExperiment expressionExperiment)
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadService.getSubSetsByDimension(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByDimension(ExpressionExperiment expressionExperiment)
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadService.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset, with assays thawed.
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment along all separating factors.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment and factor.
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment and factor, with subset characteristics initialized and assays thawed.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets for a given dataset.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets for a given dataset.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension, with assays lightly thawed.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsWithCharacteristics(ExpressionExperiment ee)	Obtain all the subsets for a given dataset.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithCharacteristics(ExpressionExperiment ee)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsWithCharacteristics(ExpressionExperiment ee)	Obtain all the subsets for a given dataset, with characteristics initialized.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsWithCharacteristics(ExpressionExperiment ee)
Taxon	ExpressionExperimentDao.getTaxon(ExpressionExperiment ee)	Determine the taxon for a given experiment or subset.
Taxon	ExpressionExperimentDaoImpl.getTaxon(ExpressionExperiment ee)
Taxon	ExpressionExperimentReadService.getTaxon(ExpressionExperiment expressionExperiment)	Included for cycle-break parity with the facade: the only read-method back-edge from ExpressionExperimentSetServiceImpl is getTaxon.
Taxon	ExpressionExperimentReadServiceImpl.getTaxon(ExpressionExperiment ee)
Taxon	ExpressionExperimentService.getTaxon(ExpressionExperiment expressionExperiment)	Returns the taxon of the given experiment.
Taxon	ExpressionExperimentServiceImpl.getTaxon(ExpressionExperiment ee)
boolean	ExpressionExperimentDao.hasProcessedExpressionData(ExpressionExperiment ee)	Test if the dataset has preferred expression data vectors.
boolean	ExpressionExperimentDaoImpl.hasProcessedExpressionData(ExpressionExperiment ee)
boolean	ExpressionExperimentService.hasProcessedExpressionData(ExpressionExperiment ee)	Test if the given experiment has processed data vectors.
boolean	ExpressionExperimentServiceImpl.hasProcessedExpressionData(ExpressionExperiment ee)
boolean	ExpressionExperimentDao.hasSingleCellQuantitationTypes(ExpressionExperiment ee)	Indicate if the given experiment has single-cell quantitation types.
boolean	ExpressionExperimentDaoImpl.hasSingleCellQuantitationTypes(ExpressionExperiment ee)
boolean	ExpressionExperimentDao.hasSourceMetadata(ExpressionExperiment ee)	Whether a source metadata document is stored for this experiment.
boolean	ExpressionExperimentDaoImpl.hasSourceMetadata(ExpressionExperiment ee)
boolean	ExpressionExperimentService.hasSourceMetadata(ExpressionExperiment ee)
boolean	ExpressionExperimentServiceImpl.hasSourceMetadata(ExpressionExperiment ee)
protected void	ExpressionExperimentDaoImpl.initializeCachedFilteringResult(ExpressionExperiment ee)
boolean	ExpressionExperimentService.isRNASeq(ExpressionExperiment expressionExperiment)
boolean	ExpressionExperimentServiceImpl.isRNASeq(ExpressionExperiment expressionExperiment)
boolean	ExpressionExperimentService.isSingleCell(ExpressionExperiment ee)	Indicate if the given experiment is a single-cell experiment.
boolean	ExpressionExperimentServiceImpl.isSingleCell(ExpressionExperiment ee)
Boolean	ExpressionExperimentService.isSuitableForDEA(ExpressionExperiment ee)
Boolean	ExpressionExperimentServiceImpl.isSuitableForDEA(ExpressionExperiment ee)
boolean	ExpressionExperimentService.isTroubled(ExpressionExperiment expressionExperiment)	Check if the dataset is either troubled or uses a troubled platform.
boolean	ExpressionExperimentServiceImpl.isTroubled(ExpressionExperiment ee)
boolean	ExpressionExperimentService.isTwoChannel(ExpressionExperiment expressionExperiment)	Deprecated. Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.
boolean	ExpressionExperimentServiceImpl.isTwoChannel(ExpressionExperiment expressionExperiment)	Deprecated.
ArrayDesignsForExperimentCache	ExpressionExperimentPrePersistService.prepare(ExpressionExperiment ee)	Call this before calling the persister.
ArrayDesignsForExperimentCache	ExpressionExperimentPrePersistService.prepare(ExpressionExperiment ee, ArrayDesignsForExperimentCache c)
ArrayDesignsForExperimentCache	ExpressionExperimentPrePersistServiceImpl.prepare(ExpressionExperiment ee)
ArrayDesignsForExperimentCache	ExpressionExperimentPrePersistServiceImpl.prepare(ExpressionExperiment ee, ArrayDesignsForExperimentCache cache)
DesignPreflightReport	ExpressionExperimentService.previewDesignChange(ExpressionExperiment ee, ExperimentalDesignValueObject proposed)	Predict what would happen if proposed were applied as the experiment's new design via PUT.
DesignPreflightReport	ExpressionExperimentService.previewDesignChange(ExpressionExperiment ee, ExperimentalDesignValueObject proposed, DesignCommitPlan plan)	Predict what would happen if proposed were applied, including the bindings a DesignCommitPlan defers to a second apply pass.
DesignPreflightReport	ExpressionExperimentServiceImpl.previewDesignChange(ExpressionExperiment ee, ExperimentalDesignValueObject proposed)
DesignPreflightReport	ExpressionExperimentServiceImpl.previewDesignChange(ExpressionExperiment ee, ExperimentalDesignValueObject proposed, DesignCommitPlan plan)
PreboardedExperimentService.PromotionResult	PreboardedExperimentService.promote(ExpressionExperiment ee, PreboardedExperiment preboarded)	Promote the preboarded to a loaded ExpressionExperiment.
PreboardedExperimentService.PromotionResult	PreboardedExperimentServiceImpl.promote(ExpressionExperiment ee, PreboardedExperiment preboarded)
SingleCellDimensionExperiment	SingleCellDimensionExperimentDao.record(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension scd)	Insert (or no-op if already present) a link row for (ee, qt, scd).
SingleCellDimensionExperiment	SingleCellDimensionExperimentDaoImpl.record(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension scd)
void	SingleCellExperimentDesignAuditService.recordCellTypeFactorCreated(ExpressionExperiment ee, ExperimentalFactor cellTypeFactor, String ctlDescription)	Record an ExperimentalDesignUpdatedEvent against the EE noting the creation of a cell-type factor from a preferred cell-type assignment.
void	SingleCellExperimentDesignAuditServiceImpl.recordCellTypeFactorCreated(ExpressionExperiment ee, ExperimentalFactor cellTypeFactor, String ctlDescription)	Record an ExperimentalDesignUpdatedEvent against the EE noting the creation of a cell-type factor from a preferred cell-type assignment.
void	SingleCellExperimentDesignAuditService.recordCellTypeFactorRemoved(ExpressionExperiment ee, ExperimentalFactor removedCellTypeFactor)	Record an ExperimentalDesignUpdatedEvent against the EE noting the removal of an existing cell-type factor.
void	SingleCellExperimentDesignAuditServiceImpl.recordCellTypeFactorRemoved(ExpressionExperiment ee, ExperimentalFactor removedCellTypeFactor)	Record an ExperimentalDesignUpdatedEvent against the EE noting the removal of an existing cell-type factor.
void	GeeqAuditService.recordGeeqScoring(ExpressionExperiment ee, String note, String detail)	Record a GeeqEvent against the given experiment with the supplied note and detail string.
void	GeeqAuditServiceImpl.recordGeeqScoring(ExpressionExperiment ee, String note, String detail)	Record a GeeqEvent against the given experiment with the supplied note and detail string.
void	ExpressionExperimentWriteAuditService.recordPreferredQtChanged(ExpressionExperiment ee, QuantitationType qt, QuantitationType previousPreferredQt, Class<? extends DataVector> vectorType)	Audit that the preferred QuantitationType for the given vector type changed to qt.
void	ExpressionExperimentWriteAuditServiceImpl.recordPreferredQtChanged(ExpressionExperiment ee, QuantitationType qt, QuantitationType previousPreferredQt, Class<? extends DataVector> vectorType)	Audit that the preferred QuantitationType for the given vector type changed to qt.
void	ExpressionExperimentWriteAuditService.recordPreferredQtCleared(ExpressionExperiment ee, QuantitationType previousPreferredQt, Class<? extends DataVector> vectorType)	Audit that the preferred QuantitationType for the given vector type was cleared (the previously-preferred QT is no longer preferred).
void	ExpressionExperimentWriteAuditServiceImpl.recordPreferredQtCleared(ExpressionExperiment ee, QuantitationType previousPreferredQt, Class<? extends DataVector> vectorType)	Audit that the preferred QuantitationType for the given vector type was cleared (the previously-preferred QT is no longer preferred).
void	ExpressionExperimentDao.refreshCurationDetails(ExpressionExperiment ee)	Reload the experiment's curation details from the database, replacing their second-level cache entry.
void	ExpressionExperimentDaoImpl.refreshCurationDetails(ExpressionExperiment ee)
CellTypeAssignment	SingleCellExpressionExperimentService.relabelCellTypes(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, List<String> newCellTypeLabels, Protocol labellingProtocol, String description, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)	Relabel the cell types of an existing set of single-cell vectors.
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.relabelCellTypes(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, List<String> newCellTypeLabels, Protocol protocol, String description, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)
ExpressionExperiment	ExpressionExperimentReadService.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentService.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentServiceImpl.reload(ExpressionExperiment ee)
SingleCellDimension	ExpressionExperimentDao.reloadSingleCellDimension(ExpressionExperiment ee, SingleCellDimension dimension)	Reload a single-cell dimension.
SingleCellDimension	ExpressionExperimentDaoImpl.reloadSingleCellDimension(ExpressionExperiment ee, SingleCellDimension dimension)
void	ExpressionExperimentDaoImpl.remove(ExpressionExperiment ee)
void	ExpressionExperimentServiceImpl.remove(ExpressionExperiment ee)	Deletes an experiment and all of its associated objects, including coexpression links.
void	ExpressionExperimentWriteService.remove(ExpressionExperiment ee)	Deletes an experiment and all of its associated objects, including coexpression links.
void	ExpressionExperimentWriteServiceImpl.remove(ExpressionExperiment ee)	Deletes an experiment and all of its associated objects, including coexpression links.
int	ExpressionExperimentDao.removeAllCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension singleCellDimension)	Remove all the cell-level characteristics of a single-cell dimension.
int	ExpressionExperimentDaoImpl.removeAllCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension singleCellDimension)
long	SingleCellExpressionExperimentService.removeAllCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
long	SingleCellExpressionExperimentServiceImpl.removeAllCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
long	SingleCellExpressionExperimentService.removeAllCellTypeAssignments(ExpressionExperiment ee, QuantitationType qt)
long	SingleCellExpressionExperimentServiceImpl.removeAllCellTypeAssignments(ExpressionExperiment ee, QuantitationType qt)
int	ExpressionExperimentDao.removeAllRawDataVectors(ExpressionExperiment ee)	Remove all raw data vectors.
int	ExpressionExperimentDaoImpl.removeAllRawDataVectors(ExpressionExperiment ee)
int	ExpressionExperimentDataVectorService.removeAllRawDataVectors(ExpressionExperiment ee)
int	ExpressionExperimentDataVectorServiceImpl.removeAllRawDataVectors(ExpressionExperiment ee)
int	ExpressionExperimentService.removeAllRawDataVectors(ExpressionExperiment ee)
int	ExpressionExperimentServiceImpl.removeAllRawDataVectors(ExpressionExperiment ee)
int	ExpressionExperimentDao.removeAllSingleCellDataVectors(ExpressionExperiment ee)	Remove all single-cell data vectors and their quantitation types.
int	ExpressionExperimentDaoImpl.removeAllSingleCellDataVectors(ExpressionExperiment ee)
Characteristic	ExpressionExperimentService.removeAnnotation(ExpressionExperiment ee, Long annotationId)	Remove a single experiment-level tag from ee by characteristic id.
Characteristic	ExpressionExperimentService.removeAnnotation(ExpressionExperiment ee, Long annotationId, String reason)	As ExpressionExperimentService.removeAnnotation(ExpressionExperiment, Long), with a caller-supplied reason appended to the audit note.
Characteristic	ExpressionExperimentServiceImpl.removeAnnotation(ExpressionExperiment ee, Long annotationId)	Per-tag REST-write counterpart to ExpressionExperimentServiceImpl.removeCharacteristics(ExpressionExperiment, Collection).
Characteristic	ExpressionExperimentServiceImpl.removeAnnotation(ExpressionExperiment ee, Long annotationId, String reason)	Reason-carrying overload; see ExpressionExperimentServiceImpl.addAnnotation(ExpressionExperiment, Characteristic, String).
int	SingleCellDimensionExperimentDao.removeByEE(ExpressionExperiment ee)	Remove every link row attached to the given EE.
int	SingleCellDimensionExperimentDaoImpl.removeByEE(ExpressionExperiment ee)
int	SingleCellDimensionExperimentDao.removeByEEAndQt(ExpressionExperiment ee, QuantitationType qt)	Remove the link row for (ee, qt), if any.
int	SingleCellDimensionExperimentDaoImpl.removeByEEAndQt(ExpressionExperiment ee, QuantitationType qt)
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, CellLevelCharacteristics clc)	Remove existing cell-level characteristics by QT.
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Remove existing cell-level characteristics.
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, CellLevelCharacteristics clc)
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristicsById(ExpressionExperiment ee, Long clcId)
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristicsById(ExpressionExperiment ee, SingleCellDimension dimension, Long clcId)
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristicsById(ExpressionExperiment ee, Long clcId)
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristicsById(ExpressionExperiment ee, SingleCellDimension dimension, Long clcId)
boolean	SingleCellExpressionExperimentService.removeCellLevelCharacteristicsByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
boolean	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristicsByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
void	SingleCellExpressionExperimentService.removeCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, CellTypeAssignment cellTypeAssignment)	Remove the given cell type assignment by QT.
void	SingleCellExpressionExperimentService.removeCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension scd, CellTypeAssignment cellTypeAssignment)	Remove the given cell type assignment.
void	SingleCellExpressionExperimentServiceImpl.removeCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, CellTypeAssignment cellTypeAssignment)
void	SingleCellExpressionExperimentServiceImpl.removeCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension dimension, CellTypeAssignment cellTypeAssignment)
void	SingleCellExpressionExperimentService.removeCellTypeAssignmentById(ExpressionExperiment ee, Long ctaId)
void	SingleCellExpressionExperimentService.removeCellTypeAssignmentById(ExpressionExperiment ee, SingleCellDimension dimension, Long ctaId)
void	SingleCellExpressionExperimentServiceImpl.removeCellTypeAssignmentById(ExpressionExperiment ee, Long ctaId)
void	SingleCellExpressionExperimentServiceImpl.removeCellTypeAssignmentById(ExpressionExperiment ee, SingleCellDimension dimension, Long ctaId)
boolean	SingleCellExpressionExperimentService.removeCellTypeAssignmentByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
boolean	SingleCellExpressionExperimentServiceImpl.removeCellTypeAssignmentByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
void	ExpressionExperimentService.removeCharacteristics(ExpressionExperiment ee, Collection<Characteristic> characteristicsToRemove)
void	ExpressionExperimentServiceImpl.removeCharacteristics(ExpressionExperiment ee, Collection<Characteristic> characteristicsToRemove)
void	ExpressionExperimentWriteService.removeCharacteristics(ExpressionExperiment ee, Collection<Characteristic> characteristicsToRemove)
void	ExpressionExperimentWriteServiceImpl.removeCharacteristics(ExpressionExperiment ee, Collection<Characteristic> characteristicsToRemove)
int	ExpressionExperimentSetService.removeFromSets(ExpressionExperiment bas)	Remove an experiment from all sets it is in.
int	ExpressionExperimentSetServiceImpl.removeFromSets(ExpressionExperiment bas)
int	ExpressionExperimentDao.removeOrphanQuantitationTypes(ExpressionExperiment ee)	Remove quantitation types attached to ee that are not referenced by any data vector.
int	ExpressionExperimentDaoImpl.removeOrphanQuantitationTypes(ExpressionExperiment ee)
int	ExpressionExperimentDao.removeProcessedDataVectors(ExpressionExperiment ee)	Remove processed data vectors.
int	ExpressionExperimentDaoImpl.removeProcessedDataVectors(ExpressionExperiment ee)
int	ExpressionExperimentDataVectorService.removeProcessedDataVectors(ExpressionExperiment ee)
int	ExpressionExperimentDataVectorServiceImpl.removeProcessedDataVectors(ExpressionExperiment ee)
int	ExpressionExperimentService.removeProcessedDataVectors(ExpressionExperiment ee)	Remove the processed data vectors for the given experiment.
int	ExpressionExperimentServiceImpl.removeProcessedDataVectors(ExpressionExperiment ee)
int	ExpressionExperimentDao.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)	Remove raw data vectors for a given quantitation type.
int	ExpressionExperimentDaoImpl.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
int	ExpressionExperimentDataVectorService.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)	Equivalent to removeRawDataVectors(ee, qt, false).
int	ExpressionExperimentDataVectorService.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
int	ExpressionExperimentDataVectorServiceImpl.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
int	ExpressionExperimentDataVectorServiceImpl.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
int	ExpressionExperimentService.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
int	ExpressionExperimentService.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
int	ExpressionExperimentServiceImpl.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
int	ExpressionExperimentServiceImpl.removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
int	ExpressionExperimentDao.removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean deleteQt)	Remove the given single-cell data vectors.
int	ExpressionExperimentDaoImpl.removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean deleteQt)
int	SingleCellExpressionExperimentService.removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)	Remove single-cell data vectors for the given quantitation type.
int	SingleCellExpressionExperimentServiceImpl.removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)
int	ExpressionExperimentDataVectorService.replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> vectors)	Replace all raw vectors on an experiment, grouping the input by QT and routing each group to either ExpressionExperimentDataVectorService.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) or ExpressionExperimentDataVectorService.addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) depending on whether the QT already exists; any QT in the experiment that is no longer represented in the input is removed.
int	ExpressionExperimentDataVectorServiceImpl.replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> newVectors)
int	ExpressionExperimentService.replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> vectors)	Used when we are replacing data, such as when converting an experiment from one platform to another.
int	ExpressionExperimentServiceImpl.replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> newVectors)
int	ExpressionExperimentDao.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Replace processed data vectors.
int	ExpressionExperimentDaoImpl.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorService.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorServiceImpl.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentService.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Replace the processed data vectors for the given experiment.
int	ExpressionExperimentServiceImpl.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDao.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)	Replace raw data vectors for a given quantitation type.
int	ExpressionExperimentDaoImpl.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorService.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorServiceImpl.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)
int	ExpressionExperimentService.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> vectors)
int	ExpressionExperimentServiceImpl.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)
int	SingleCellExpressionExperimentService.replaceSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)	Replace existing single-cell data vectors for the given quantitation type.
int	SingleCellExpressionExperimentServiceImpl.replaceSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details, boolean removeOrRecreateCellTypeFactor, boolean ignoreCompatibleFactor)
Optional<Stream<String>>	SingleCellExpressionExperimentService.streamCellIds(ExpressionExperiment ee, boolean createNewSession)
Stream<String>	SingleCellExpressionExperimentService.streamCellIds(ExpressionExperiment ee, QuantitationType qt, boolean createNewSession)
Optional<Stream<String>>	SingleCellExpressionExperimentServiceImpl.streamCellIds(ExpressionExperiment ee, boolean createNewSession)
Stream<String>	SingleCellExpressionExperimentServiceImpl.streamCellIds(ExpressionExperiment ee, QuantitationType qt, boolean createNewSession)
Stream<Characteristic>	SingleCellExpressionExperimentService.streamCellLevelCharacteristics(ExpressionExperiment ee, CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	SingleCellExpressionExperimentServiceImpl.streamCellLevelCharacteristics(ExpressionExperiment ee, CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	SingleCellExpressionExperimentService.streamCellTypes(ExpressionExperiment ee, CellTypeAssignment cta, boolean createNewSession)
Stream<Characteristic>	SingleCellExpressionExperimentServiceImpl.streamCellTypes(ExpressionExperiment ee, CellTypeAssignment cta, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDao.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)	Obtain a stream over the vectors for a given QT.
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDao.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, boolean includeBiologicalCharacteristics, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, boolean includeBiologicalCharacteristics, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)	Obtain a stream over single-cell vectors for a given quantitation type.
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
void	ExpressionExperimentDao.thaw(ExpressionExperiment expressionExperiment)	Thaw everything.
void	ExpressionExperimentDaoImpl.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadService.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadService.thawBioAssays(ExpressionExperiment expressionExperiment)	Narrow thaw used by the /samples REST endpoint: initializes only the bioAssays collection and applies Thaws.thawBioAssay(BioAssay) to each assay (which warms the array design, original platform, and biomaterial-with-factor-values shape that BioAssayValueObject reads).
ExpressionExperiment	ExpressionExperimentReadServiceImpl.thawBioAssays(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thawBioAssays(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thawBioAssays(ExpressionExperiment expressionExperiment)
void	ExpressionExperimentDao.thawLite(ExpressionExperiment expressionExperiment)	Thaw experiment metadata and bioassays.
void	ExpressionExperimentDaoImpl.thawLite(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentReadService.thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thawLite(ExpressionExperiment expressionExperiment)
void	ExpressionExperimentDao.thawLiter(ExpressionExperiment expressionExperiment)	Thaw experiment metadata.
void	ExpressionExperimentDaoImpl.thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadService.thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thawLiter(ExpressionExperiment expressionExperiment)
int	ExpressionExperimentService.updateAnnotations(ExpressionExperiment ee, Collection<Characteristic> desired)	Replace the experiment-level characteristic set on ee with the supplied desired collection (idempotent set semantics).
int	ExpressionExperimentServiceImpl.updateAnnotations(ExpressionExperiment ee, Collection<Characteristic> desired)	Idempotent set-replace for an EE's direct characteristic set.
MeanVarianceRelation	ExpressionExperimentDao.updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
MeanVarianceRelation	ExpressionExperimentDaoImpl.updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
MeanVarianceRelation	ExpressionExperimentService.updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
MeanVarianceRelation	ExpressionExperimentServiceImpl.updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
MeanVarianceRelation	ExpressionExperimentWriteService.updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
MeanVarianceRelation	ExpressionExperimentWriteServiceImpl.updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
boolean	ExpressionExperimentService.updateNameAndDescription(ExpressionExperiment ee, String name, String description)	Update the curator-editable "basics" of ee: its name (title) and/or description.
boolean	ExpressionExperimentServiceImpl.updateNameAndDescription(ExpressionExperiment ee, String name, String description)
void	ExpressionExperimentService.updatePublications(ExpressionExperiment ee, BibliographicReference primaryPublication, Collection<BibliographicReference> otherRelevantPublications)	Replace the publications associated with ee: set (or clear) its primary publication and replace its other-relevant-publication set in one shot (idempotent set semantics).
void	ExpressionExperimentService.updatePublications(ExpressionExperiment ee, PublicationAssertion primaryPublication, Collection<PublicationAssertion> otherRelevantPublications, Collection<PublicationAssertion> rejectedPublications)	Replace ee's publications and the evidence behind them in one transaction, including the record of which publications have been ruled out.
void	ExpressionExperimentServiceImpl.updatePublications(ExpressionExperiment ee, BibliographicReference primaryPublication, Collection<BibliographicReference> otherRelevantPublications)	Replace an EE's primary + other-relevant publications, recording every one as a bare curator assertion.
void	ExpressionExperimentServiceImpl.updatePublications(ExpressionExperiment ee, PublicationAssertion primaryPublication, Collection<PublicationAssertion> otherRelevantPublications, Collection<PublicationAssertion> rejectedPublications)	Replace an EE's publications and the evidence behind them.
void	ExpressionExperimentService.updateQuantitationType(ExpressionExperiment ee, QuantitationType qt, QuantitationType previousPreferredQt)	Update a quantitation type.
void	ExpressionExperimentServiceImpl.updateQuantitationType(ExpressionExperiment ee, QuantitationType qt, QuantitationType previousPreferredQt)
void	ExpressionExperimentWriteService.updateQuantitationType(ExpressionExperiment ee, QuantitationType qt, QuantitationType previousPreferredQt)
void	ExpressionExperimentWriteServiceImpl.updateQuantitationType(ExpressionExperiment ee, QuantitationType qt, QuantitationType previousPreferredQt)
void	ExpressionExperimentDao.updateSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)	Update a single-cell dimensino for a given experiment.
void	ExpressionExperimentDaoImpl.updateSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)
void	SingleCellExpressionExperimentService.updateSparsityMetrics(ExpressionExperiment ee)	Update the sparsity metrics.
void	SingleCellExpressionExperimentServiceImpl.updateSparsityMetrics(ExpressionExperiment ee)

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Collection<ArrayDesign>	ExpressionExperimentDao.getArrayDesignsUsed(Collection<ExpressionExperiment> ees)
Collection<ArrayDesign>	ExpressionExperimentDaoImpl.getArrayDesignsUsed(Collection<ExpressionExperiment> ees)
Map<ExpressionExperiment, Collection<ArrayDesign>>	ExpressionExperimentDao.getArrayDesignsUsedByExperiment(Collection<ExpressionExperiment> ees)	Per-experiment map variant of ExpressionExperimentDao.getArrayDesignsUsed(Collection): one HQL covers all supplied EEs, the result preserves which platform belongs to which EE.
Map<ExpressionExperiment, Collection<ArrayDesign>>	ExpressionExperimentDaoImpl.getArrayDesignsUsedByExperiment(Collection<ExpressionExperiment> ees)
Map<ExpressionExperiment, Collection<ArrayDesign>>	ExpressionExperimentService.getArrayDesignsUsedByExperiment(Collection<ExpressionExperiment> expressionExperiments)	Per-experiment map of array designs used: one HQL covers all supplied EEs and the result preserves which platform belongs to which EE.
Map<ExpressionExperiment, Collection<ArrayDesign>>	ExpressionExperimentServiceImpl.getArrayDesignsUsedByExperiment(Collection<ExpressionExperiment> expressionExperiments)
Map<Long,Date>	ExpressionExperimentDao.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<Long,Date>	ExpressionExperimentDaoImpl.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<Long,Date>	ExpressionExperimentReadService.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<Long,Date>	ExpressionExperimentReadServiceImpl.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<Long,Date>	ExpressionExperimentService.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<Long,Date>	ExpressionExperimentServiceImpl.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<BioAssayDimension>>	ExpressionExperimentDao.getProcessedBioAssayDimensions(Collection<ExpressionExperiment> ees)	Batched variant of ExpressionExperimentDao.getProcessedBioAssayDimensions(ExpressionExperiment) — one HQL with an IN clause for the supplied experiments.
Map<ExpressionExperiment, Collection<BioAssayDimension>>	ExpressionExperimentDaoImpl.getProcessedBioAssayDimensions(Collection<ExpressionExperiment> ees)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentDao.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentDaoImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentReadService.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentReadServiceImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentService.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<AuditEvent>>	ExpressionExperimentServiceImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentDao.getSubSetsByExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)	Batched variant of ExpressionExperimentDao.getSubSets(ExpressionExperiment): obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentDaoImpl.getSubSetsByExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)	Batched variant of ExpressionExperimentService.getSubSetsWithBioAssays(ExpressionExperiment): obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadService.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)	Batched variant: obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment, Taxon>	ExpressionExperimentDao.getTaxa(Collection<ExpressionExperiment> ees)
Map<ExpressionExperiment, Taxon>	ExpressionExperimentDaoImpl.getTaxa(Collection<ExpressionExperiment> ees)
Map<ExpressionExperiment, Taxon>	ExpressionExperimentService.getTaxa(Collection<ExpressionExperiment> ees)	Return the taxon for each of the given experiments.
Map<ExpressionExperiment, Taxon>	ExpressionExperimentServiceImpl.getTaxa(Collection<ExpressionExperiment> ees)
ExpressionExperimentSet	ExpressionExperimentSetService.initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments, Taxon taxon)
ExpressionExperimentSet	ExpressionExperimentSetServiceImpl.initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments, Taxon taxon)	Instantiate non-persistent experiment set with description = "Automatically generated for ## EEs.".
void	ExpressionExperimentServiceImpl.remove(Collection<ExpressionExperiment> entities)
void	ExpressionExperimentWriteService.remove(Collection<ExpressionExperiment> entities)
void	ExpressionExperimentWriteServiceImpl.remove(Collection<ExpressionExperiment> entities)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.maintenance

Methods in ubic.gemma.persistence.service.maintenance with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
int	TableMaintenanceUtil.updateAnnotationRelationEntries(ExpressionExperiment ee)	Rebuild the ANNOTATION_RELATION rows a curator already wrote.
int	TableMaintenanceUtilImpl.updateAnnotationRelationEntries(ExpressionExperiment ee)	Removes the CURATED rows.
int	TableMaintenanceUtil.updateExpressionExperiment2ArrayDesignEntries(ExpressionExperiment ee)
int	TableMaintenanceUtilImpl.updateExpressionExperiment2ArrayDesignEntries(ExpressionExperiment ee)
int	TableMaintenanceUtil.updateExpressionExperiment2CharacteristicEntries(ExpressionExperiment ee, Class<?> level)	Update the EXPRESSION_EXPERIMENT2CHARACTERISTIC table for a specific experiment.
int	TableMaintenanceUtilImpl.updateExpressionExperiment2CharacteristicEntries(ExpressionExperiment ee, Class<?> level)

Uses of ExpressionExperiment in ubic.gemma.persistence.service.pipeline

Method parameters in ubic.gemma.persistence.service.pipeline with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
PipelineJobBatch	PipelineJobBatchService.submit(String pipeline, Collection<ExpressionExperiment> experiments, Contact submittedBy, String paramsJson, String note)	Create a batch + one job per experiment, dispatch each to the configured scheduler.
PipelineJobBatch	PipelineJobBatchServiceImpl.submit(String pipeline, Collection<ExpressionExperiment> experiments, Contact submittedBy, String paramsJson, String note)

Uses of ExpressionExperiment in ubic.gemma.persistence.util

Subclasses with type arguments of type ExpressionExperiment in ubic.gemma.persistence.util

Modifier and Type	Class	Description
class	EntityUrlBuilder.ExpressionExperimentUrl
class	EntityUrlBuilder.ExpressionExperimentWebUrl

Methods in ubic.gemma.persistence.util that return ExpressionExperiment

Modifier and Type	Method	Description
static ExpressionExperiment	CommonQueries.getExperiment(@MayBeUninitialized BioAssaySet bas)	Resolve a BioAssaySet to the ExpressionExperiment that owns its data: itself if it is one, its source experiment if it is a subset.

Methods in ubic.gemma.persistence.util that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
static Map<ExpressionExperiment, Collection<ArrayDesign>>	CommonQueries.getArrayDesignsUsedByExperiment(Collection<? extends @MayBeUninitialized BioAssaySet> ees, Session session)	Retrieve, in one query, a per-experiment map of array designs used.

Methods in ubic.gemma.persistence.util with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
EntityUrlBuilder.ExpressionExperimentUrl	EntityUrlBuilder.EntityUrlChooser.entity(ExpressionExperiment entity)

Uses of ExpressionExperiment in ubic.gemma.rest

Methods in ubic.gemma.rest with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
HeatmapDataValueObject	HeatmapDataService.buildHeatmapData(ExpressionExperiment ee, Collection<Long> geneIds, Collection<Long> probeIds, Long resultSetId, double threshold, Integer pcaComponent, int pcaCount, int sampleSize, String encoding, Long subSetId, QuantitationType quantitationType, boolean maskOutliers)	Build a heatmap payload for ee given a vector-selection mode.

Method parameters in ubic.gemma.rest with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Object	DatasetsWebService.getBlacklistedDatasets(FilterArg<ExpressionExperiment> filterArg, SortArg<ExpressionExperiment> sortArg, OffsetArg offset, LimitArg limit, CursorArg cursorArg)	Browse blacklisted datasets.
Object	DatasetsWebService.getBlacklistedDatasets(FilterArg<ExpressionExperiment> filterArg, SortArg<ExpressionExperiment> sortArg, OffsetArg offset, LimitArg limit, CursorArg cursorArg)	Browse blacklisted datasets.
DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject<DatasetsWebService.ExpressionExperimentWithSearchResultValueObject>	DatasetsWebService.getDatasets(QueryArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, SortArg<ExpressionExperiment> sortArg)
DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject<DatasetsWebService.ExpressionExperimentWithSearchResultValueObject>	DatasetsWebService.getDatasets(QueryArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, SortArg<ExpressionExperiment> sortArg)
DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<DatasetsWebService.AnnotationWithUsageStatisticsValueObject>	DatasetsWebService.getDatasetsAnnotationsUsageStatistics(QueryArg query, FilterArg<ExpressionExperiment> filter, ExcludeArg<DatasetsWebService.AnnotationWithUsageStatisticsValueObject> exclude, LimitArg limitArg, Integer minFrequency, String category, StringArrayArg excludedCategoryUris, Boolean excludeFreeTextCategories, StringArrayArg excludedTermUris, Boolean excludeFreeTextTerms, Boolean excludeUncategorizedTerms, Boolean retainMentionedTerms, Boolean includePredicates, Boolean includeObjects)
Object	DatasetsWebService.getDatasetsByIds(DatasetArrayArg datasetsArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort, CursorArg cursorArg)	Retrieves all datasets matching the given identifiers.
Object	DatasetsWebService.getDatasetsByIds(DatasetArrayArg datasetsArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort, CursorArg cursorArg)	Retrieves all datasets matching the given identifiers.
DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<DatasetsWebService.CategoryWithUsageStatisticsValueObject>	DatasetsWebService.getDatasetsCategoriesUsageStatistics(QueryArg query, FilterArg<ExpressionExperiment> filter, LimitArg limit, StringArrayArg excludedCategoryUris, Boolean excludeFreeTextCategories, StringArrayArg excludedTermUris, Boolean excludeFreeTextTerms, Boolean excludeUncategorizedTerms, Boolean retainMentionedTerms)
Object	DatasetsWebService.getDatasetsDifferentialExpressionAnalysisResultsForGene(GeneArg<?> geneArg, QueryArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offsetArg, LimitArg limitArg, Double threshold, jakarta.ws.rs.core.HttpHeaders headers)	Obtain differential expression analysis results for a given gene.
Object	DatasetsWebService.getDatasetsDifferentialExpressionAnalysisResultsForGeneInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg, QueryArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offsetArg, LimitArg limitArg, Double threshold, jakarta.ws.rs.core.HttpHeaders headers)	Obtain differential expression analysis results for a given gene in a given taxon.
Object	DatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg<?> geneArg, QueryArg queryArg, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, CursorArg cursorArg, Boolean precise)	Retrieve the expression levels of a given gene across all datasets.
Object	DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg, QueryArg queryArg, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, CursorArg cursorArg, Boolean precise)	Retrieve the expression levels of a given gene and taxon across all datasets.
DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject>	DatasetsWebService.getDatasetsPlatformsUsageStatistics(QueryArg query, FilterArg<ExpressionExperiment> filter, LimitArg limit)
DatasetsWebService.QueriedAndFilteredAndInferredResponseDataObject<DatasetsWebService.TaxonWithUsageStatisticsValueObject>	DatasetsWebService.getDatasetsTaxaUsageStatistics(QueryArg query, FilterArg<ExpressionExperiment> filterArg)
ResponseDataObject<Long>	DatasetsWebService.getNumberOfAnnotations(QueryArg query, FilterArg<ExpressionExperiment> filter, String category, Integer minFrequency, Boolean excludeFreeText)
ResponseDataObject<Long>	DatasetsWebService.getNumberOfDatasets(QueryArg query, FilterArg<ExpressionExperiment> filter)
ResponseDataObject<Long>	DatasetsWebService.getNumberOfSamples(FilterArg<ExpressionExperiment> filter)
Object	TaxaWebService.getTaxonDatasets(TaxonArg<?> taxonArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort, CursorArg cursorArg)	Retrieves datasets for the given taxon.
Object	TaxaWebService.getTaxonDatasets(TaxonArg<?> taxonArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort, CursorArg cursorArg)	Retrieves datasets for the given taxon.
jakarta.ws.rs.core.Response	DatasetsWebService.refreshDatasetsAnnotations(QueryArg query, FilterArg<ExpressionExperiment> filter, ExcludeArg<DatasetsWebService.AnnotationWithUsageStatisticsValueObject> exclude, LimitArg limitArg, Integer minFrequency, String category, StringArrayArg excludedCategoryUris, Boolean excludeFreeTextCategories, StringArrayArg excludedTermUris, Boolean excludeFreeTextTerms, Boolean excludeUncategorizedTerms, Boolean retainMentionedTerms, Boolean includePredicates, Boolean includeObjects)
jakarta.ws.rs.core.Response	DatasetsWebService.refreshDatasetsPlatforms(QueryArg query, FilterArg<ExpressionExperiment> filter, LimitArg limit)
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasets(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)	Does a search for datasets containing characteristics matching the given string.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasets(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)	Does a search for datasets containing characteristics matching the given string.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasetsByQueryInPath(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasetsByQueryInPath(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasets(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Same as AnnotationsWebService.searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasets(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Same as AnnotationsWebService.searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasetsByQueryInPath(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasetsByQueryInPath(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)

Constructors in ubic.gemma.rest with parameters of type ExpressionExperiment

Modifier	Constructor	Description
	DatasetMetadataFileValueObject(ExpressionExperimentMetaFileType type, ExpressionExperiment ee)

Constructor parameters in ubic.gemma.rest with type arguments of type ExpressionExperiment

Modifier	Constructor	Description
	ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject vo, SearchResult<ExpressionExperiment> result, String resultObjectUrl, boolean resultObjectUrlExternal)

Uses of ExpressionExperiment in ubic.gemma.rest.util.args

Subclasses with type arguments of type ExpressionExperiment in ubic.gemma.rest.util.args

Modifier and Type	Class	Description
class	DatasetArg<T>	Mutable argument type base class for dataset (ExpressionExperiment) API.
class	DatasetArgService
class	DatasetArrayArg

Methods in ubic.gemma.rest.util.args that return types with arguments of type ExpressionExperiment

Modifier and Type	Method	Description
List<SearchResult<ExpressionExperiment>>	DatasetArgService.getResultsForSearchQuery(QueryArg query, Highlighter highlighter, Collection<Throwable> queryWarnings)	Obtain the search results for a given query and highlighter.

Methods in ubic.gemma.rest.util.args with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
QuantitationType	QuantitationTypeArgService.getEntity(QuantitationTypeArg<?> quantitationTypeArg, ExpressionExperiment ee)
QuantitationType	QuantitationTypeArgService.getEntity(QuantitationTypeArg<?> quantitationTypeArg, ExpressionExperiment ee, Class<? extends DesignElementDataVector> vectorType)
void	DatasetArgService.populateOutliers(ExpressionExperiment ee, Collection<BioAssayValueObject> bioAssayValueObjects)	Set BioAssayValueObject.getPredictedOutlier() from the median-correlation algorithm.

Method parameters in ubic.gemma.rest.util.args with type arguments of type ExpressionExperiment

Modifier and Type	Method	Description
Filters	DatasetArgService.getFilters(FilterArg<ExpressionExperiment> filterArg)
Filters	DatasetArgService.getFilters(FilterArg<ExpressionExperiment> filterArg, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms)
Filters	DatasetArgService.getFilters(FilterArg<ExpressionExperiment> filterArg, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)