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.util
ubic.gemma.core.analysis.expression
ubic.gemma.core.analysis.expression.coexpression.links
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.filter
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.report
ubic.gemma.core.analysis.service
ubic.gemma.core.analysis.singleCell.aggregate	This packge contains classes for splitting 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.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.coexp
ubic.gemma.core.tasks.analysis.diffex
ubic.gemma.core.tasks.analysis.expression
ubic.gemma.core.tasks.maintenance
ubic.gemma.core.visualization
ubic.gemma.model.common.quantitationtype
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.analysis.expression.coexpression
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.bioAssayData
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.expression.experiment

Uses of ExpressionExperiment in ubic.gemma.apps

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

Modifier and Type	Method	Description
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	DetectQuantitationTypeCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	DifferentialExpressionAnalysisCli.processExpressionExperiment(ExpressionExperiment ee)
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	ExpressionExperimentDataFileGeneratorCli.processExpressionExperiment(ExpressionExperiment ee1)
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	LinkAnalysisCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	ListQuantitationTypesCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected void	LockExpressionDataFileCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	OrderVectorsByDesignCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	ProcessedDataComputeCLI.processExpressionExperiment(ExpressionExperiment ee)
protected void	RefreshExperimentCli.processExpressionExperiment(ExpressionExperiment bas)
protected void	ReplaceDataCli.processExpressionExperiment(ExpressionExperiment ee)
protected void	RNASeqBatchInfoCli.processExpressionExperiment(ExpressionExperiment ee)	Deprecated.
protected void	RNASeqDataAddCli.processExpressionExperiment(ExpressionExperiment ee)
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	VectorMergingCli.processExpressionExperiment(ExpressionExperiment expressionExperiment)
protected abstract void	ExpressionExperimentVectorsManipulatingCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)	Process a set of vectors identified by a QuantitationType.
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	SingleCellDataAggregateDeleterCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt)
protected void	SingleCellDataAggregatorCli.processExpressionExperimentVectors(ExpressionExperiment expressionExperiment, QuantitationType qt)
protected void	SingleCellDataDeleterCli.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 refreshProcessedVectors, boolean refreshReports)	Refresh a dataset for Gemma Web.
protected Serializable	ExpressionExperimentManipulatingCLI.toBatchObject(ExpressionExperiment object)

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)
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> 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> 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.coexpression.links

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

Modifier and Type	Method	Description
LinkAnalysis	LinkAnalysisService.process(ExpressionExperiment ee, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)	Run a link analysis on an experiment, and persist the results if the configuration says to.
LinkAnalysis	LinkAnalysisServiceImpl.process(ExpressionExperiment ee, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)

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

Constructor	Description
UnsuitableForAnalysisException(ExpressionExperiment ee, String string)

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	DifferentialExpressionAnalyzerServiceImpl.deleteAnalyses(ExpressionExperiment expressionExperiment)
void	DifferentialExpressionAnalyzerService.deleteAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis existingAnalysis)	Deletes the given analysis.
void	DifferentialExpressionAnalyzerServiceImpl.deleteAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis existingAnalysis)
void	DifferentialExpressionAnalyzerServiceImpl.deleteStatistics(ExpressionExperiment ee, DifferentialExpressionAnalysis analysis)	Remove old files which will otherwise be cruft.
Collection<ExpressionAnalysisResultSet>	DifferentialExpressionAnalyzerService.extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate)	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)
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.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis copyMe, boolean persist)	Redo
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis copyMe, boolean persist)
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
Collection<RawExpressionDataVector>	TwoChannelMissingValues.computeMissingValues(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	TwoChannelMissingValues.computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)
Collection<RawExpressionDataVector>	TwoChannelMissingValuesImpl.computeMissingValues(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	TwoChannelMissingValuesImpl.computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)
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)
Collection<OutlierDetails>	OutlierDetectionService.getOutlierDetails(ExpressionExperiment ee)	Obtain existing outlier details from a previous OutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment) invocation.
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)
void	VectorMergingService.mergeVectors(ExpressionExperiment expExp)
void	VectorMergingServiceImpl.mergeVectors(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	TwoChannelMissingValueHelperService.persist(ExpressionExperiment source, Collection<RawExpressionDataVector> results)
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)
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

Constructor	Description
FilteringRelatedPreprocessingException(ExpressionExperiment ee, FilteringException cause)
InsufficientProbesException(ExpressionExperiment ee, String message)
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 with parameters of type ExpressionExperiment

Modifier and Type	Method	Description
boolean	ExpressionExperimentBatchCorrectionService.checkCorrectability(ExpressionExperiment ee)	Is there a Batch factor provided?
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)
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)
ExperimentalFactor	ExpressionExperimentBatchCorrectionService.getBatchFactor(ExpressionExperiment ee)	For convenience of some testing classes
ExperimentalFactor	ExpressionExperimentBatchCorrectionServiceImpl.getBatchFactor(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)
static ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionServiceImpl.removeOutliers(ExpressionDataDoubleMatrix originalDataMatrix, ExpressionExperiment ee)	Remove outlier samples from the data matrix, based on outliers that were flagged in the experiment (not just candidate outliers)

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

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.filter

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

Constructor	Description
InsufficientDataException(ExpressionExperiment ee, String message)
InsufficientSamplesException(ExpressionExperiment ee, String message)

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

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)
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.hasPca(ExpressionExperiment ee)
boolean	SVDServiceImpl.hasPca(ExpressionExperiment ee)
SVDResult	SVDService.svd(ExpressionExperiment ee)
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
void	ExpressionExperimentReportService.recalculateExperimentBatchInfo(ExpressionExperiment ee)	Recalculates the batch effect and batch confound information for the given dataset.
void	ExpressionExperimentReportServiceImpl.recalculateExperimentBatchInfo(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, boolean forceWrite)	Copy a MultiQC report.
Path	ExpressionDataFileServiceImpl.copyMultiQCReport(ExpressionExperiment ee, Path existingFile, 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)
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)
static String	ExpressionDataFileUtils.getEEFolderName(ExpressionExperiment ee)	Forms a folder name where the given experiments metadata will be located (within the #metadataDir directory).
static String	ExpressionDataFileUtils.getEigenGenesFilename(ExpressionExperiment ee)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)
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)
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	CoexpressionWriter.write(ExpressionExperiment ee, Collection<CoexpressionValueObject> geneLinks, Writer writer)
void	ExpressionDataFileService.writeDesignMatrix(ExpressionExperiment ee, Writer writer)	Writes out the experimental design for the given experiment.
void	ExpressionDataFileServiceImpl.writeDesignMatrix(ExpressionExperiment ee, Writer writer)
int	ExpressionDataFileService.writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, int fetchSize, boolean forceWrite, Path destDir)
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 forceWrite, Path destDir)	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 forceWrite, Path destDir)
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 forceWrite, Path destDir)
int	ExpressionDataFileServiceImpl.writeMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, OutputStream stream)
LockedPath	ExpressionDataFileService.writeOrLocateCoexpressionDataFile(ExpressionExperiment ee, boolean forceWrite)	Write or located the coexpression data file for a given experiment
LockedPath	ExpressionDataFileServiceImpl.writeOrLocateCoexpressionDataFile(ExpressionExperiment ee, boolean forceWrite)
Optional<LockedPath>	ExpressionDataFileService.writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite)	Locate or create an experimental design file for a given experiment.
Optional<LockedPath>	ExpressionDataFileService.writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite, long timeout, TimeUnit timeUnit)
Optional<LockedPath>	ExpressionDataFileServiceImpl.writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite)
Optional<LockedPath>	ExpressionDataFileServiceImpl.writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite, long timeout, TimeUnit timeUnit)
Collection<LockedPath>	ExpressionDataFileService.writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee, boolean forceWrite)	Locate or create the differential expression data file(s) for a given experiment.
Collection<LockedPath>	ExpressionDataFileServiceImpl.writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee, boolean forceWrite)
Optional<LockedPath>	ExpressionDataFileService.writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)
Optional<LockedPath>	ExpressionDataFileServiceImpl.writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)
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 forceWrite)	Write single-cell expression data to a standard location for a given quantitation type.
LockedPath	ExpressionDataFileServiceImpl.writeOrLocateMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean forceWrite)
Future<Path>	ExpressionDataFileService.writeOrLocateMexSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean forceWrite)
Future<Path>	ExpressionDataFileServiceImpl.writeOrLocateMexSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, 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)
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)
LockedPath	ExpressionDataFileService.writeOrLocateTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean forceWrite)	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 forceWrite)
Future<Path>	ExpressionDataFileService.writeOrLocateTabularSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean forceWrite)
Future<Path>	ExpressionDataFileServiceImpl.writeOrLocateTabularSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean forceWrite)
int	ExpressionDataFileService.writeProcessedExpressionData(ExpressionExperiment ee, boolean filtered, ScaleType scaleType, 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, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeProcessedExpressionData(ExpressionExperiment ee, boolean filtered, ScaleType scaleType, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeProcessedExpressionData(ExpressionExperiment ee, List<BioAssay> samples, boolean filtered, ScaleType scaleType, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeRawExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, 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, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeTabularSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, int fetchSize, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, int fetchSize, Writer writer, boolean autoFlush)	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, int fetchSize, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, int fetchSize, Writer writer, boolean autoFlush)

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	SingleCellExpressionExperimentAggregatorService.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, AggregateConfig config)	Aggregate preferred single-cell data vectors by the given cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentAggregatorServiceImpl.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellType2Factor, AggregateConfig config)
QuantitationType	SingleCellExpressionExperimentAggregatorService.aggregateVectorsByCellType(ExpressionExperiment ee, List<BioAssay> cellBAs, AggregateConfig config)	Aggregate preferred single-cell data vectors by the preferred cell type assignment and the only cell type factor of the experiment.
QuantitationType	SingleCellExpressionExperimentAggregatorServiceImpl.aggregateVectorsByCellType(ExpressionExperiment ee, List<BioAssay> cellBAs, AggregateConfig config)
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateService.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, AggregateConfig config)	Re-aggregate a dataset by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateServiceImpl.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, AggregateConfig config)
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateService.redoAggregateByCellType(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType previousQt, AggregateConfig config)	Re-aggregate a dataset by cell type.
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateServiceImpl.redoAggregateByCellType(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType previousQt, AggregateConfig config)
int	SingleCellExpressionExperimentAggregatorService.removeAggregatedVectors(ExpressionExperiment ee, QuantitationType qt)	Remove aggregated vectors for the given quantitation type.
int	SingleCellExpressionExperimentAggregatorService.removeAggregatedVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)	Remove aggregated vectors for the given quantitation type.
int	SingleCellExpressionExperimentAggregatorServiceImpl.removeAggregatedVectors(ExpressionExperiment ee, QuantitationType qt)
int	SingleCellExpressionExperimentAggregatorServiceImpl.removeAggregatedVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitService.split(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, SplitConfig config)	Split biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitServiceImpl.split(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> mappedCellTypeFactors, SplitConfig config)
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateService.splitAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics cta, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SplitConfig splitConfig, AggregateConfig config)	Split and aggregate by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateServiceImpl.splitAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SplitConfig splitConfig, AggregateConfig config)
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateService.splitAndAggregateByCellType(ExpressionExperiment expressionExperiment, SplitConfig splitConfig, AggregateConfig config)	Split and aggregate by cell type.
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateServiceImpl.splitAndAggregateByCellType(ExpressionExperiment expressionExperiment, SplitConfig splitConfig, AggregateConfig config)
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitService.splitByCellType(ExpressionExperiment ee, SplitConfig config)	Split a single-cell dataset by cell type.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitServiceImpl.splitByCellType(ExpressionExperiment ee, SplitConfig config)

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

Fields in ubic.gemma.core.datastructure.matrix declared as ExpressionExperiment

Modifier and Type	Field	Description
protected ExpressionExperiment	BaseExpressionDataMatrix.expressionExperiment

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

Modifier and Type	Method	Description
ExpressionExperiment	BaseExpressionDataMatrix.getExpressionExperiment()
ExpressionExperiment	BulkExpressionDataMatrix.getExpressionExperiment()	The experiment this matrix is associated with, if known.
ExpressionExperiment	ExpressionDataMatrix.getExpressionExperiment()	Return the expression experiment this matrix is holding data for.
ExpressionExperiment	SingleCellExpressionDataDoubleMatrix.getExpressionExperiment()
ExpressionExperiment	SingleCellExpressionDataIntMatrix.getExpressionExperiment()
ExpressionExperiment	TwoChannelExpressionDataMatrixBuilder.getExpressionExperiment()

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

Modifier and Type	Method	Description
static Collection<QuantitationType>	TwoChannelExpressionDataMatrixBuilder.getMissingValueQuantitationTypes(ExpressionExperiment expressionExperiment)
static Collection<QuantitationType>	TwoChannelExpressionDataMatrixBuilder.getPreferredAndMissingQuantitationTypes(ExpressionExperiment expressionExperiment)
static Collection<QuantitationType>	TwoChannelExpressionDataMatrixBuilder.getPreferredQuantitationTypes(ExpressionExperiment expressionExperiment)
static Collection<QuantitationType>	TwoChannelExpressionDataMatrixBuilder.getUsefulQuantitationTypes(ExpressionExperiment expressionExperiment)
protected Collection<BulkExpressionDataVector>	BaseExpressionDataMatrix.selectVectors(ExpressionExperiment ee, QuantitationType quantitationType)

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

Constructor	Description
ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors)
ExpressionDataDoubleMatrix(ExpressionExperiment ee, QuantitationType qt, DoubleMatrix<CompositeSequence,BioMaterial> matrix)	Create a matrix given a 'raw' matrix that uses the same samples as the experiment.
ExpressionDataStringMatrix(ExpressionExperiment expressionExperiment, Collection<CompositeSequence> designElements, QuantitationType quantitationType)
ExpressionDataStringMatrix(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)

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, Writer buf)	Appends base header information (about the experiment) to a file.
void	ExperimentalDesignWriter.write(Writer writer, ExpressionExperiment ee, boolean writeHeader)
void	ExperimentalDesignWriter.write(Writer writer, ExpressionExperiment ee, Collection<BioAssay> bioAssays, boolean writeBaseHeader, boolean writeHeader)

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)

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.
void	DataDeleterService.deleteProcessedData(ExpressionExperiment ee)
void	DataDeleterServiceImpl.deleteProcessedData(ExpressionExperiment ee)
void	DataDeleterService.deleteRawData(ExpressionExperiment ee, QuantitationType qt)
void	DataDeleterServiceImpl.deleteRawData(ExpressionExperiment ee, QuantitationType qt)
void	DataDeleterService.deleteSingleCellData(ExpressionExperiment ee, QuantitationType qt)
void	DataDeleterServiceImpl.deleteSingleCellData(ExpressionExperiment ee, QuantitationType qt)
void	DataDeleterService.deleteSingleCellDataAggregate(ExpressionExperiment ee, QuantitationType qt)
void	DataDeleterServiceImpl.deleteSingleCellDataAggregate(ExpressionExperiment ee, QuantitationType qt)
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	ExperimentPlatformSwitchHelperService.persist(ExpressionExperiment expExp, ArrayDesign arrayDesign)
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

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.geo

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	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. anything that is not a cell type assignment), the data type is automatically detected.
Collection<CellLevelCharacteristics>	SingleCellDataLoaderService.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e. anything that is not a cell type assignment).
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)

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)
Collection<SearchResult<ExpressionExperiment>>	DatabaseSearchSource.searchExpressionExperiment(SearchSettings settings)	Does search on exact string by: id, name and short name.
Collection<SearchResult<ExpressionExperiment>>	HibernateSearchSource.searchExpressionExperiment(SearchSettings settings)
Collection<SearchResult<ExpressionExperiment>>	OntologySearchSource.searchExpressionExperiment(SearchSettings settings)	Search via characteristics i.e. ontology terms.

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

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

Modifier and Type	Method	Description
ExpressionExperiment	LinkAnalysisTaskCommand.getExpressionExperiment()

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

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

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

Constructor	Description
LinkAnalysisTaskCommand(ExpressionExperiment ee, LinkAnalysisConfig lac, FilterConfig fg)

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

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	PreprocessTaskCommand.getExpressionExperiment()
ExpressionExperiment	SvdTaskCommand.getExpressionExperiment()
ExpressionExperiment	TwoChannelMissingValueTaskCommand.getExpressionExperiment()

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

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

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

Constructor	Description
BatchInfoFetchTaskCommand(ExpressionExperiment expressionExperiment)
PreprocessTaskCommand(ExpressionExperiment ee)
SvdTaskCommand(ExpressionExperiment expressionExperiment)
SvdTaskCommand(ExpressionExperiment expressionExperiment, boolean postProcessOnly)
TwoChannelMissingValueTaskCommand(ExpressionExperiment ee)
TwoChannelMissingValueTaskCommand(ExpressionExperiment expressionExperiment, double s2n, Collection<Double> extraMissingValueIndictors)

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

Constructor	Description
ExpressionExperimentReportTaskCommand(ExpressionExperiment expressionExperiment)

Uses of ExpressionExperiment in ubic.gemma.core.visualization

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

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.model.common.quantitationtype

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

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.expression.bioAssayData

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

Modifier and Type	Method	Description
void	MeanVarianceRelation.setSecurityOwner(ExpressionExperiment ee)

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

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

Modifier and Type	Method	Description
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)
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

Constructor	Description
ExpressionExperimentDetailsValueObject(ExpressionExperiment ee)
ExpressionExperimentDetailsValueObject(ExpressionExperiment ee, gemma.gsec.acl.domain.AclObjectIdentity aoi, gemma.gsec.acl.domain.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, gemma.gsec.acl.domain.AclObjectIdentity aoi, gemma.gsec.acl.domain.AclSid sid)	Creates a new ExpressionExperiment value object with additional information about ownership.

Uses of ExpressionExperiment in ubic.gemma.persistence.persister

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

Modifier and Type	Method	Description
ExpressionExperiment	ExpressionPersister.persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
ExpressionExperiment	PersisterHelper.persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
protected ExpressionExperiment	ExpressionPersister.persistExpressionExperiment(ExpressionExperiment ee, AbstractPersister.Caches caches)

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

Modifier and Type	Method	Description
ExpressionExperiment	ExpressionPersister.persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
ExpressionExperiment	PersisterHelper.persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
protected ExpressionExperiment	ExpressionPersister.persistExpressionExperiment(ExpressionExperiment ee, AbstractPersister.Caches caches)
ArrayDesignsForExperimentCache	ExpressionPersister.prepare(ExpressionExperiment ee)
ArrayDesignsForExperimentCache	PersisterHelper.prepare(ExpressionExperiment ee)

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)

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

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

Modifier and Type	Method	Description
void	CoexpressionAnalysisService.addCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment, CoexpCorrelationDistribution coexpd)	For backfilling of the coexpression distributions from flat files - remove when no longer needed.
void	CoexpressionAnalysisServiceImpl.addCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment, CoexpCorrelationDistribution coexpd)
CoexpCorrelationDistribution	CoexpressionAnalysisDao.getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)
CoexpCorrelationDistribution	CoexpressionAnalysisDaoImpl.getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)
CoexpCorrelationDistribution	CoexpressionAnalysisService.getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)
CoexpCorrelationDistribution	CoexpressionAnalysisServiceImpl.getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)
boolean	CoexpressionAnalysisDao.hasCoexpCorrelationDistribution(ExpressionExperiment ee)
boolean	CoexpressionAnalysisDaoImpl.hasCoexpCorrelationDistribution(ExpressionExperiment ee)
boolean	CoexpressionAnalysisService.hasCoexpCorrelationDistribution(ExpressionExperiment ee)
boolean	CoexpressionAnalysisServiceImpl.hasCoexpCorrelationDistribution(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.getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)

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)
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>	PrincipalComponentAnalysisService.getTopLoadedProbes(ExpressionExperiment ee, int component, int count)
List<ProbeLoading>	PrincipalComponentAnalysisServiceImpl.getTopLoadedProbes(ExpressionExperiment ee, int component, int count)
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)

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)
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<ExpressionExperiment>>>	CharacteristicDao.findExperimentReferencesByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)	Similar to CharacteristicDao.findExperimentsByUris(Collection, Taxon, int, boolean), but returns proxies with instead of initializing all the EEs in bulk.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicDaoImpl.findExperimentReferencesByUris(Collection<String> uris, 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, 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, Taxon taxon, int limit, boolean rankByLevel)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicService.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicServiceImpl.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<ExpressionExperiment,BibliographicReference>	BibliographicReferenceDao.getAllExperimentLinkedReferences()
Map<ExpressionExperiment,BibliographicReference>	BibliographicReferenceDaoImpl.getAllExperimentLinkedReferences()
Map<ExpressionExperiment,BibliographicReference>	BibliographicReferenceService.getAllExperimentLinkedReferences()	Return all the BibRefs that are linked to ExpressionExperiments.
Map<ExpressionExperiment,BibliographicReference>	BibliographicReferenceServiceImpl.getAllExperimentLinkedReferences()
Map<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceDao.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceDaoImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceService.getRelatedExperiments(Collection<BibliographicReference> records)
Collection<ExpressionExperiment>	BibliographicReferenceService.getRelatedExperiments(BibliographicReference bibliographicReference)	Get the ExpressionExperiments, if any, that are linked to the given reference.
Map<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceServiceImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Collection<ExpressionExperiment>	BibliographicReferenceServiceImpl.getRelatedExperiments(BibliographicReference bibRef)

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	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>	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>>	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>	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	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	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	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	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>	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>	ArrayDesignService.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignServiceImpl.getExpressionExperiments(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.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
int	ProcessedExpressionDataVectorDao.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)	Populate the processed data for the given experiment.
int	ProcessedExpressionDataVectorDaoImpl.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)
int	ProcessedExpressionDataVectorService.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks)	Create processed vectors and optionally update ranks.
int	ProcessedExpressionDataVectorService.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks, boolean ignoreQuantitationMismatch)	Create processed vectors and optionally update ranks.
int	ProcessedExpressionDataVectorServiceImpl.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks)
int	ProcessedExpressionDataVectorServiceImpl.createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks, boolean ignoreQuantitationMismatch)
void	ProcessedExpressionDataVectorService.evictFromCache(ExpressionExperiment ee)
void	ProcessedExpressionDataVectorServiceImpl.evictFromCache(ExpressionExperiment ee)
Collection<T>	AbstractDesignElementDataVectorDao.findByExpressionExperiment(ExpressionExperiment ee)
Collection<T>	DesignElementDataVectorDao.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)
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>>	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
Collection<BioMaterial>	BioMaterialDao.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialDaoImpl.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialService.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialServiceImpl.findByExperiment(ExpressionExperiment experiment)

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

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

Modifier and Type	Method	Description
ExpressionExperiment	ExpressionExperimentDaoImpl.find(ExpressionExperiment entity)
ExpressionExperiment	ExpressionExperimentDao.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentService.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentDao.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentService.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentDao.findByFactor(ExperimentalFactor ef)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactor(ExperimentalFactor ef)
ExpressionExperiment	ExpressionExperimentService.findByFactor(ExperimentalFactor factor)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactor(ExperimentalFactor factor)
ExpressionExperiment	ExpressionExperimentDao.findByFactorValue(Long factorValueId)
ExpressionExperiment	ExpressionExperimentDao.findByFactorValue(FactorValue fv)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactorValue(Long factorValueId)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactorValue(FactorValue fv)
ExpressionExperiment	ExpressionExperimentService.findByFactorValue(Long factorValueId)
ExpressionExperiment	ExpressionExperimentService.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactorValue(Long factorValueId)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentDao.findByQuantitationType(QuantitationType quantitationType)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByQuantitationType(QuantitationType quantitationType)
ExpressionExperiment	ExpressionExperimentService.findByQuantitationType(QuantitationType type)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByQuantitationType(QuantitationType type)
ExpressionExperiment	ExpressionExperimentDao.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentService.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByShortName(String shortName)
ExpressionExperiment	ExpressionExperimentDao.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentDaoImpl.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentService.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentServiceImpl.findOneByAccession(String accession)
ExpressionExperiment	ExpressionExperimentDao.findOneByName(String name)
ExpressionExperiment	ExpressionExperimentDaoImpl.findOneByName(String name)
ExpressionExperiment	ExpressionExperimentService.findOneByName(String name)
ExpressionExperiment	ExpressionExperimentServiceImpl.findOneByName(String name)
ExpressionExperiment	ExperimentalDesignDao.getExpressionExperiment(ExperimentalDesign experimentalDesign)
ExpressionExperiment	ExperimentalDesignDaoImpl.getExpressionExperiment(ExperimentalDesign experimentalDesign)
ExpressionExperiment	ExperimentalDesignService.getExpressionExperiment(ExperimentalDesign experimentalDesign)	Gets the expression experiment for the specified experimental design object
ExpressionExperiment	ExperimentalDesignServiceImpl.getExpressionExperiment(ExperimentalDesign experimentalDesign)
ExpressionExperiment	ExperimentalDesignDao.getExpressionExperimentById(Long experimentalDesignId)
ExpressionExperiment	ExperimentalDesignDaoImpl.getExpressionExperimentById(Long experimentalDesignId)
ExpressionExperiment	ExperimentalDesignService.getExpressionExperimentById(Long experimentalDesignId)	Gets the expression experiment for the specified experimental design object
ExpressionExperiment	ExperimentalDesignServiceImpl.getExpressionExperimentById(Long experimentalDesignId)
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	ExpressionExperimentService.loadAndThaw(Long id)	Load an experiment and thaw it as per ExpressionExperimentService.thaw(ExpressionExperiment).
ExpressionExperiment	ExpressionExperimentServiceImpl.loadAndThaw(Long id)
<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, String message)
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	ExpressionExperimentService.loadAndThawOrFail(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.loadAndThawOrFail(Long id, Function<String,T> exceptionSupplier, String message)
ExpressionExperiment	ExpressionExperimentService.loadReference(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadReference(Long id)
ExpressionExperiment	ExpressionExperimentService.loadWithAuditTrail(Long id)	Load an experiment with its audit trail initialized.
ExpressionExperiment	ExpressionExperimentServiceImpl.loadWithAuditTrail(Long id)
ExpressionExperiment	ExpressionExperimentService.loadWithCharacteristics(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadWithCharacteristics(Long id)
ExpressionExperiment	ExpressionExperimentService.loadWithMeanVarianceRelation(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadWithMeanVarianceRelation(Long id)
ExpressionExperiment	ExpressionExperimentService.loadWithPrimaryPublication(Long id)
ExpressionExperiment	ExpressionExperimentServiceImpl.loadWithPrimaryPublication(Long id)
ExpressionExperiment	SingleCellExpressionExperimentService.loadWithSingleCellVectors(Long id)	Load an experiment with its single-cell data vectors initialized.
ExpressionExperiment	SingleCellExpressionExperimentServiceImpl.loadWithSingleCellVectors(Long id)
ExpressionExperiment	ExpressionExperimentService.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentServiceImpl.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentService.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thawLite(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>	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>	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>	ExpressionExperimentService.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByBioMaterial(BioMaterial bm)
Map<ExpressionExperiment,Collection<BioMaterial>>	ExpressionExperimentDao.findByBioMaterials(Collection<BioMaterial> bms)
Map<ExpressionExperiment,Collection<BioMaterial>>	ExpressionExperimentDaoImpl.findByBioMaterials(Collection<BioMaterial> bms)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByExpressedGene(Gene gene, Double rank)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByExpressedGene(Gene gene, Double rank)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByExpressedGene(Gene gene, double rank)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByExpressedGene(Gene gene, double rank)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentDao.findByFactorValues(Collection<FactorValue> fvs)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentDaoImpl.findByFactorValues(Collection<FactorValue> fvs)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentService.findByFactorValues(Collection<FactorValue> factorValues)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentServiceImpl.findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByGene(Gene gene)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.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>	ExpressionExperimentService.findByName(String name)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByName(String name)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByTaxon(Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.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>	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>	ExpressionExperimentService.findUpdatedAfter(Date date)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findUpdatedAfter(Date date)
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()
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.getExperimentsLackingPublications()
Collection<ExpressionExperiment>	ExpressionExperimentService.getExperimentsLackingPublications()
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.getExperimentsLackingPublications()
Collection<ExpressionExperiment>	ExpressionExperimentDao.getExperimentsWithOutliers()
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.getExperimentsWithOutliers()
Collection<ExpressionExperiment>	ExpressionExperimentService.getExperimentsWithOutliers()
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.getExperimentsWithOutliers()
Map<ExpressionExperiment,Collection<AuditEvent>>	ExpressionExperimentDao.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment,Collection<AuditEvent>>	ExpressionExperimentDaoImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment,Collection<AuditEvent>>	ExpressionExperimentService.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment,Collection<AuditEvent>>	ExpressionExperimentServiceImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Collection<ExpressionExperiment>	ExpressionExperimentService.loadAllReferences()	Load references for all experiments.
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.loadAllReferences()
Collection<ExpressionExperiment>	ExpressionExperimentDao.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentService.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.loadLackingFactors()
Collection<ExpressionExperiment>	ExpressionExperimentDao.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentService.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.loadLackingTags()
Collection<ExpressionExperiment>	ExpressionExperimentService.loadReferences(Collection<Long> ids)	Load references for the given experiment IDs.
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.loadReferences(Collection<Long> ids)
List<ExpressionExperiment>	ExpressionExperimentDao.loadWithRelationsAndCache(List<Long> ids)	Load datasets by IDs with the same relation as CachedFilteringDao.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
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)
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.addCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, CellTypeAssignment cta)
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)	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)
FactorValue	ExpressionExperimentService.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentServiceImpl.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)
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	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)	Add single-cell data vectors.
int	SingleCellExpressionExperimentServiceImpl.addSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)
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)
int	ExpressionExperimentDao.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Add processed data vectors
int	ExpressionExperimentDaoImpl.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.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)
ExpressionExperiment	ExpressionExperimentDaoImpl.find(ExpressionExperiment entity)
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>	ExpressionExperimentService.getAnnotations(ExpressionExperiment ee)	Retrieve annotations for a given experiment.
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperiment expressionExperiment)
Collection<ArrayDesign>	ExpressionExperimentDao.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)
Collection<ArrayDesign>	ExpressionExperimentDaoImpl.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)
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 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)
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>	ExpressionExperimentDaoImpl.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentService.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentServiceImpl.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentDao.getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)	Retrieve BioAssayDimension that are used by subsets of a given ExpressionExperiment.
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentService.getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)	Retrieve all the dimensions that are linked to the subsets of the given experiment.
Collection<BioAssayDimension>	ExpressionExperimentServiceImpl.getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)
BioAssayDimension	ExpressionExperimentService.getBioAssayDimensionWithAssays(ExpressionExperiment ee, QuantitationType qt)	Obtain a BioAssayDimension with its assays initialized as per Thaws.thawBioAssay(BioAssay).
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimensionWithAssays(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	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.
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)
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)
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)
Category	SingleCellExpressionExperimentService.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
Category	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
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)
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)
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)
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)
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)
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)
Date	ExpressionExperimentDao.getLastArrayDesignUpdate(ExpressionExperiment ee)
Date	ExpressionExperimentDaoImpl.getLastArrayDesignUpdate(ExpressionExperiment ee)
Date	ExpressionExperimentService.getLastArrayDesignUpdate(ExpressionExperiment expressionExperiment)
Date	ExpressionExperimentServiceImpl.getLastArrayDesignUpdate(ExpressionExperiment ee)
Map<BioAssay,Long>	ExpressionExperimentDao.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<BioAssay,Long>	ExpressionExperimentDaoImpl.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)	Obtain the number of non-zeroes by sample.
Map<BioAssay,Long>	ExpressionExperimentDaoImpl.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize)
Map<BioAssay,Long>	SingleCellExpressionExperimentService.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize)
Map<BioAssay,Long>	SingleCellExpressionExperimentServiceImpl.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize)
long	ExpressionExperimentDao.getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)	Obtain the number of single-cell vectors for a given QT.
long	ExpressionExperimentDaoImpl.getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)
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)	Obtain the preferred assignment of the preferred single-cell vectors.
CellTypeAssignment	ExpressionExperimentDaoImpl.getPreferredCellTypeAssignment(ExpressionExperiment ee)
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)
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)
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)
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>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)
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)
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>>	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	ExpressionExperimentDaoImpl.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>	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 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 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)
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 includeCharacteristics, boolean includeIndices)
List<SingleCellDimension>	ExpressionExperimentDaoImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	ExpressionExperimentDaoImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeCharacteristics, boolean includeIndices)
List<SingleCellDimension>	SingleCellExpressionExperimentService.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	SingleCellExpressionExperimentService.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeCharacteristics, boolean includeIndices)
List<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeCharacteristics, boolean includeIndices)
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 includeCharacteristics, boolean includeIndices)
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, 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)
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	ExpressionExperimentService.getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID.
ExpressionExperimentSubSet	ExpressionExperimentServiceImpl.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)
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>>	ExpressionExperimentService.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.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<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)
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>	ExpressionExperimentService.getSubSetsWithCharacteristics(ExpressionExperiment ee)	Obtain all the subsets for a given dataset.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithCharacteristics(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)
protected void	ExpressionExperimentDaoImpl.initializeCachedFilteringResult(ExpressionExperiment ee)
boolean	ExpressionExperimentService.isRNASeq(ExpressionExperiment expressionExperiment)
boolean	ExpressionExperimentServiceImpl.isRNASeq(ExpressionExperiment expressionExperiment)
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)
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)
ExperimentalFactor	SingleCellExpressionExperimentService.recreateCellTypeFactor(ExpressionExperiment ee)	Recreate the cell type factor based on the preferred labelling of the preferred single-cell vectors.
ExperimentalFactor	SingleCellExpressionExperimentServiceImpl.recreateCellTypeFactor(ExpressionExperiment ee)
CellTypeAssignment	SingleCellExpressionExperimentService.relabelCellTypes(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, List<String> newCellTypeLabels, Protocol labellingProtocol, String description)	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)
ExpressionExperiment	ExpressionExperimentService.reload(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentServiceImpl.reload(ExpressionExperiment ee)
void	ExpressionExperimentDaoImpl.remove(ExpressionExperiment ee)
void	ExpressionExperimentServiceImpl.remove(ExpressionExperiment ee)	Deletes an experiment and all of its associated objects, including coexpression links.
int	ExpressionExperimentDao.removeAllRawDataVectors(ExpressionExperiment ee)	Remove all raw data vectors.
int	ExpressionExperimentDaoImpl.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)
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.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)
int	ExpressionExperimentDao.removeProcessedDataVectors(ExpressionExperiment ee)	Remove processed data vectors.
int	ExpressionExperimentDaoImpl.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	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	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	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	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)	Replace existing single-cell data vectors for the given quantitation type.
int	SingleCellExpressionExperimentServiceImpl.replaceSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)
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 createNewSession)	Obtain a stream over the vectors for a given QT.
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDao.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, 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 createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
void	ExpressionExperimentDao.thaw(ExpressionExperiment expressionExperiment)	Thaw everything.
void	ExpressionExperimentDaoImpl.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thaw(ExpressionExperiment expressionExperiment)
void	ExpressionExperimentDao.thawLite(ExpressionExperiment expressionExperiment)	Thaw experiment metadata and bioassays.
void	ExpressionExperimentDaoImpl.thawLite(ExpressionExperiment ee)
ExpressionExperiment	ExpressionExperimentService.thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thawLite(ExpressionExperiment expressionExperiment)
void	ExpressionExperimentDao.thawLiter(ExpressionExperiment expressionExperiment)	Thaw experiment metadata.
void	ExpressionExperimentDaoImpl.thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentService.thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment	ExpressionExperimentServiceImpl.thawLiter(ExpressionExperiment expressionExperiment)
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)
void	ExpressionExperimentService.updateQuantitationType(ExpressionExperiment ee, QuantitationType qt)	Update a quantitation type.
void	ExpressionExperimentServiceImpl.updateQuantitationType(ExpressionExperiment ee, QuantitationType qt)
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
Map<Long,Date>	ExpressionExperimentDao.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<Long,Date>	ExpressionExperimentDaoImpl.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<Long,Date>	ExpressionExperimentService.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<Long,Date>	ExpressionExperimentServiceImpl.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment,Collection<AuditEvent>>	ExpressionExperimentDao.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment,Collection<AuditEvent>>	ExpressionExperimentDaoImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment,Collection<AuditEvent>>	ExpressionExperimentService.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<ExpressionExperiment,Collection<AuditEvent>>	ExpressionExperimentServiceImpl.getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
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)

Uses of ExpressionExperiment in ubic.gemma.persistence.util

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

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

Modifier and Type	Method	Description
DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	DatasetsWebService.getBlacklistedDatasets(FilterArg<ExpressionExperiment> filterArg, SortArg<ExpressionExperiment> sortArg, OffsetArg offset, LimitArg limit)	Browse blacklisted datasets.
DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	DatasetsWebService.getBlacklistedDatasets(FilterArg<ExpressionExperiment> filterArg, SortArg<ExpressionExperiment> sortArg, OffsetArg offset, LimitArg limit)	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)
DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	DatasetsWebService.getDatasetsByIds(DatasetArrayArg datasetsArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Retrieves all datasets matching the given identifiers.
DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	DatasetsWebService.getDatasetsByIds(DatasetArrayArg datasetsArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	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, javax.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, javax.ws.rs.core.HttpHeaders headers)	Obtain differential expression analysis results for a given gene in a given taxon.
PaginatedResponseDataObject<ExperimentExpressionLevelsValueObject>	DatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg<?> geneArg, QueryArg queryArg, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate)	Retrieve the expression levels of a given gene across all datasets.
PaginatedResponseDataObject<ExperimentExpressionLevelsValueObject>	DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg, QueryArg queryArg, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate)	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.getNumberOfDatasets(QueryArg query, FilterArg<ExpressionExperiment> filter)
FilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	TaxaWebService.getTaxonDatasets(TaxonArg<?> taxonArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Retrieves datasets for the given taxon.
FilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	TaxaWebService.getTaxonDatasets(TaxonArg<?> taxonArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Retrieves datasets for the given taxon.
javax.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)
javax.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)

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

Constructor	Description
ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject vo, SearchResult<ExpressionExperiment> result)

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

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)

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)

Uses of ExpressionExperiment in ubic.gemma.web.controller.expression.experiment

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

Modifier and Type	Method	Description
static boolean	ExpressionExperimentQCUtils.hasNodeDegreeDistFile(ExpressionExperiment ee)
static boolean	ExpressionExperimentQCUtils.hasPvalueDistFiles(ExpressionExperiment ee)
static int	ExpressionExperimentQCUtils.numFactors(ExpressionExperiment expressionExperiment)

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

Modifier and Type	Method	Description
Collection<AnnotationValueObject>	ExpressionExperimentController.getAnnotation(EntityDelegator<ExpressionExperiment> e)	AJAX
Collection<BioMaterialValueObject>	ExperimentalDesignController.getBioMaterials(EntityDelegator<ExpressionExperiment> e)
Collection<DesignMatrixRowValueObject>	ExpressionExperimentController.getDesignMatrixRows(EntityDelegator<ExpressionExperiment> e)	AJAX
Collection<ExperimentalFactorValueObject>	ExpressionExperimentController.getExperimentalFactors(EntityDelegator<ExpressionExperiment> e)	AJAX