Uses of Class ubic.gemma.model.expression.experiment.ExpressionExperiment (Gemma 1.31.13 API)

Packages that use ExpressionExperiment
Package	Description
ubic.gemma.core.analysis.expression
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess
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.apps
ubic.gemma.core.datastructure.matrix
ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.loader.expression
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.simple
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
ubic.gemma.web.util

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
`Collection<DifferentialExpressionAnalysis>`	AnalysisSelectionAndExecutionService.`analyze(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)`
`Collection<DifferentialExpressionAnalysis>`	AnalysisSelectionAndExecutionServiceImpl.`analyze(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)`
`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)`
`abstract Collection<DifferentialExpressionAnalysis>`	AbstractDifferentialExpressionAnalyzer.`run(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)`
`abstract Collection<DifferentialExpressionAnalysis>`	AbstractDifferentialExpressionAnalyzer.`run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)`
`Collection<DifferentialExpressionAnalysis>`	DiffExAnalyzer.`run(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)`
`Collection<DifferentialExpressionAnalysis>`	DiffExAnalyzer.`run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)`	Allows entry of modified data matrices into the workflow.
`Collection<DifferentialExpressionAnalysis>`	LinearModelAnalyzer.`run(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)`
`Collection<DifferentialExpressionAnalysis>`	LinearModelAnalyzer.`run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)`
`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 that return ExpressionExperiment
Modifier and Type	Method	Description
`ExpressionExperiment`	ExpressionDataMatrixBuilder.`getExpressionExperiment()`

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)`
`static Collection<QuantitationType>`	ExpressionDataMatrixBuilder.`getMissingValueQuantitationTypes(ExpressionExperiment expressionExperiment)`
`Collection<OutlierDetails>`	OutlierDetectionService.`getOutlierDetails(ExpressionExperiment ee)`	Obtain existing outlier details from a previous `OutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment)` invocation.
`Collection<OutlierDetails>`	OutlierDetectionServiceImpl.`getOutlierDetails(ExpressionExperiment ee)`
`static Collection<QuantitationType>`	ExpressionDataMatrixBuilder.`getPreferredAndMissingQuantitationTypes(ExpressionExperiment expressionExperiment)`
`static Collection<QuantitationType>`	ExpressionDataMatrixBuilder.`getPreferredQuantitationTypes(ExpressionExperiment expressionExperiment)`
`static Collection<QuantitationType>`	ExpressionDataMatrixBuilder.`getUsefulQuantitationTypes(ExpressionExperiment expressionExperiment)`
`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
`FailedToComputeSingularValueDecomposition(ExpressionExperiment ee, SVDException cause)`
`InsufficientProbesException(ExpressionExperiment ee, String message)`
`PreprocessingException(ExpressionExperiment ee, String message)`
`PreprocessingException(ExpressionExperiment ee, String message, Throwable cause)`
`PreprocessingException(ExpressionExperiment ee, Throwable cause)`
`QuantitationMismatchPreprocessingException(ExpressionExperiment ee, QuantitationMismatchException 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? Is there a confound problem? Do we have at least two samples per batch? This will return true even if there is evidence the data has been batch-corrected before; we assume the caller wants to redo it based on the raw data
`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)`
`BatchEffectType`	ExpressionExperimentBatchInformationService.`getBatchEffect(ExpressionExperiment ee)`	Obtain a `BatchEffectType` describing the batch effect state of the given experiment.
`BatchEffectType`	ExpressionExperimentBatchInformationServiceImpl.`getBatchEffect(ExpressionExperiment ee)`
`BatchEffectDetails`	ExpressionExperimentBatchInformationService.`getBatchEffectDetails(ExpressionExperiment ee)`	Obtain the full batch effect details of a given experiment.
`BatchEffectDetails`	ExpressionExperimentBatchInformationServiceImpl.`getBatchEffectDetails(ExpressionExperiment ee)`
`String`	ExpressionExperimentBatchInformationService.`getBatchEffectStatistics(ExpressionExperiment ee)`	Obtain a string describing the summary statistics of a batch effect is present in the given experiment.
`String`	ExpressionExperimentBatchInformationServiceImpl.`getBatchEffectStatistics(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<LocalFile> 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
`FilteringException(ExpressionExperiment ee, String message)`
`InsufficientDataException(ExpressionExperiment ee, String message)`
`InsufficientSamplesException(ExpressionExperiment ee, String message)`
`NoRowsLeftAfterFilteringException(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>`	SVDServiceHelper.`getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)`
`Set<ExperimentalFactor>`	SVDServiceHelperImpl.`getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)`
`Map<ProbeLoading,DoubleVectorValueObject>`	SVDServiceHelper.`getTopLoadedVectors(ExpressionExperiment ee, int component, int count)`
`Map<ProbeLoading,DoubleVectorValueObject>`	SVDServiceHelperImpl.`getTopLoadedVectors(ExpressionExperiment ee, int component, int count)`
`boolean`	SVDServiceHelper.`hasPca(ExpressionExperiment ee)`
`boolean`	SVDServiceHelperImpl.`hasPca(ExpressionExperiment ee)`
`SVDResult`	SVDServiceHelper.`retrieveSvd(ExpressionExperiment ee)`
`SVDResult`	SVDServiceHelperImpl.`retrieveSvd(ExpressionExperiment ee)`	Get the SVD information for experiment with id given.
`SVDResult`	SVDServiceHelper.`svd(ExpressionExperiment ee)`
`SVDResult`	SVDServiceHelperImpl.`svd(ExpressionExperiment ee)`
`SVDResult`	SVDServiceHelper.`svdFactorAnalysis(ExpressionExperiment ee)`	Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
`SVDResult`	SVDServiceHelperImpl.`svdFactorAnalysis(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`	ExpressionDataFileService.`deleteAllFiles(ExpressionExperiment ee)`	Delete any existing coexpression, data, or differential expression data files.
`void`	ExpressionDataFileServiceImpl.`deleteAllFiles(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)`
`File`	ExpressionDataFileService.`getMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type)`	Locate a metadata file.
`File`	ExpressionDataFileServiceImpl.`getMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixService.`getProcessedExpressionDataMatrix(ExpressionExperiment ee)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixServiceImpl.`getProcessedExpressionDataMatrix(ExpressionExperiment ee)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixService.`getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)`	Obtain a raw expression data matrix for a given quantitation type
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixServiceImpl.`getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)`
`Optional<File>`	ExpressionDataFileService.`writeOrLocateCoexpressionDataFile(ExpressionExperiment ee, boolean forceWrite)`	Write or located the coexpression data file for a given experiment
`Optional<File>`	ExpressionDataFileServiceImpl.`writeOrLocateCoexpressionDataFile(ExpressionExperiment ee, boolean forceWrite)`
`File`	ExpressionDataFileService.`writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite)`	Locate or create an experimental design file for a given experiment.
`File`	ExpressionDataFileServiceImpl.`writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite)`
`Collection<File>`	ExpressionDataFileService.`writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee, boolean forceWrite)`	Locate or create the differential expression data file(s) for a given experiment.
`Collection<File>`	ExpressionDataFileServiceImpl.`writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee, boolean forceWrite)`
`Optional<File>`	ExpressionDataFileService.`writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)`
`Optional<File>`	ExpressionDataFileServiceImpl.`writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)`
`File`	ExpressionDataFileService.`writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)`
`File`	ExpressionDataFileServiceImpl.`writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)`
`Optional<File>`	ExpressionDataFileService.`writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)`	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<File>`	ExpressionDataFileServiceImpl.`writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)`
`File`	ExpressionDataFileService.`writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)`	Locate or create a new data file for the given quantitation type.
`File`	ExpressionDataFileServiceImpl.`writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)`
`void`	ExpressionDataFileService.`writeProcessedExpressionData(ExpressionExperiment ee, Writer writer)`	Write processed expression data to a given writer for a given quantitation type.
`void`	ExpressionDataFileServiceImpl.`writeProcessedExpressionData(ExpressionExperiment ee, Writer writer)`
`Optional<File>`	ExpressionDataFileService.`writeProcessedExpressionDataFile(ExpressionExperiment ee, boolean filtered, String fileName, boolean compress)`	Create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).
`Optional<File>`	ExpressionDataFileServiceImpl.`writeProcessedExpressionDataFile(ExpressionExperiment ee, boolean filtered, String fileName, boolean compress)`
`void`	ExpressionDataFileService.`writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, Writer writer)`	Write raw expression data to a given writer for a given quantitation type.
`void`	ExpressionDataFileServiceImpl.`writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, Writer writer)`
`void`	ExpressionDataFileServiceImpl.`writeTsv(ExpressionExperiment entity, Writer writer)`

Uses of ExpressionExperiment in ubic.gemma.core.apps

Methods in ubic.gemma.core.apps that return ExpressionExperiment
Modifier and Type	Method	Description
`protected ExpressionExperiment`	ExperimentalDesignImportCli.`locateExpressionExperiment(String shortName)`

Methods in ubic.gemma.core.apps with parameters of type ExpressionExperiment
Modifier and Type	Method	Description
`protected void`	ExpressionExperimentManipulatingCLI.`refreshExpressionExperimentFromGemmaWeb(ExpressionExperiment ee, boolean refreshVectors, boolean refreshReports)`	Refresh a dataset for Gemma Web.

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

Methods in ubic.gemma.core.datastructure.matrix that return ExpressionExperiment
Modifier and Type	Method	Description
`ExpressionExperiment`	BaseExpressionDataMatrix.`getExpressionExperiment()`	The associated `ExpressionExperiment`, if known.
`ExpressionExperiment`	ExpressionDataMatrix.`getExpressionExperiment()`	Return the expression experiment this matrix is holding data for.

Methods in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionExperiment
Modifier and Type	Method	Description
`static void`	ExpressionDataWriterUtils.`appendBaseHeader(ExpressionExperiment experiment, boolean design, StringBuffer buf)`	Appends base header information (about the experiment) to a file.
`static void`	ExpressionDataWriterUtils.`appendBaseHeader(ExpressionExperiment experiment, String fileTypeStr, StringBuffer 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)`

Constructors in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionExperiment
Constructor	Description
`ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> 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.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, Integer readLength, Boolean isPairedReads, boolean allowMissingSamples)`
`void`	DataUpdaterImpl.`addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Integer readLength, Boolean isPairedReads, 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`	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<LocalFile> 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.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> matrix)`
`ExpressionExperiment`	SimpleExpressionDataLoaderServiceImpl.`convert(SimpleExpressionExperimentMetaData metaData, DoubleMatrix<String,String> matrix)`
`ExpressionExperiment`	SimpleExpressionDataLoaderService.`create(SimpleExpressionExperimentMetaData metaData, InputStream data)`	Parses, converts (into Gemma objects), and loads data into the database.
`ExpressionExperiment`	SimpleExpressionDataLoaderServiceImpl.`create(SimpleExpressionExperimentMetaData metaData, InputStream data)`

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.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.

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(String taskId, 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
`protected void`	ExperimentalDesignVisualizationServiceImpl.`plotExperimentalDesign(ExpressionExperiment e)`	Test method for now, shows how this can be used.

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 DesignElementDataVector> 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 that return ExpressionExperiment
Modifier and Type	Method	Description
`ExpressionExperiment`	DataVector.`getExpressionExperiment()`

Methods in ubic.gemma.model.expression.bioAssayData with parameters of type ExpressionExperiment
Modifier and Type	Method	Description
`void`	DataVector.`setExpressionExperiment(ExpressionExperiment expressionExperiment)`
`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
`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)`	Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.
`QuantitationType`	QuantitationTypeDaoImpl.`find(ExpressionExperiment ee, QuantitationType quantitationType)`
`QuantitationType`	QuantitationTypeService.`find(ExpressionExperiment ee, QuantitationType quantitationType)`	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)`
`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.`loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)`
`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)`
`List<QuantitationTypeValueObject>`	QuantitationTypeDaoImpl.`loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment ee)`	Load `QuantitationTypeValueObject` in the context of an associated expression experiment.
`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`	ProcessedExpressionDataVectorService.`computeProcessedExpressionData(ExpressionExperiment ee)`	Create processed vectors and update ranks.
`int`	ProcessedExpressionDataVectorService.`computeProcessedExpressionData(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)`	Create processed vectors and update ranks.
`int`	ProcessedExpressionDataVectorServiceImpl.`computeProcessedExpressionData(ExpressionExperiment ee)`
`int`	ProcessedExpressionDataVectorServiceImpl.`computeProcessedExpressionData(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)`
`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)`
`int`	ProcessedExpressionDataVectorService.`createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)`
`int`	ProcessedExpressionDataVectorServiceImpl.`createProcessedDataVectors(ExpressionExperiment expressionExperiment)`
`int`	ProcessedExpressionDataVectorServiceImpl.`createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)`
`Collection<T>`	AbstractDesignElementDataVectorDao.`findByExpressionExperiment(ExpressionExperiment ee)`
`Collection<T>`	DesignElementDataVectorDao.`findByExpressionExperiment(ExpressionExperiment ee)`
`Collection<RawExpressionDataVector>`	RawExpressionDataVectorDao.`findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)`
`Collection<RawExpressionDataVector>`	RawExpressionDataVectorDaoImpl.`findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)`
`Collection<RawExpressionDataVector>`	RawExpressionDataVectorService.`findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)`
`Collection<RawExpressionDataVector>`	RawExpressionDataVectorServiceImpl.`findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)`
`Collection<DoubleVectorValueObject>`	ProcessedExpressionDataVectorService.`getProcessedDataArrays(ExpressionExperiment expressionExperiment)`
`Collection<DoubleVectorValueObject>`	ProcessedExpressionDataVectorServiceImpl.`getProcessedDataArrays(ExpressionExperiment expressionExperiment)`
`Collection<ProcessedExpressionDataVector>`	ProcessedExpressionDataVectorService.`getProcessedDataVectors(ExpressionExperiment expressionExperiment)`
`Collection<ProcessedExpressionDataVector>`	ProcessedExpressionDataVectorServiceImpl.`getProcessedDataVectors(ExpressionExperiment expressionExperiment)`
`Collection<ProcessedExpressionDataVector>`	ProcessedExpressionDataVectorService.`getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)`	Retrieve and thaw a collection of vectors for a given experiment.
`Collection<ProcessedExpressionDataVector>`	ProcessedExpressionDataVectorServiceImpl.`getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)`
`Collection<ProcessedExpressionDataVector>`	ProcessedExpressionDataVectorDao.`getProcessedVectors(ExpressionExperiment expressionExperiment)`
`Collection<ProcessedExpressionDataVector>`	ProcessedExpressionDataVectorDaoImpl.`getProcessedVectors(ExpressionExperiment ee)`
`Collection<DoubleVectorValueObject>`	ProcessedExpressionDataVectorService.`getRandomProcessedDataArrays(ExpressionExperiment ee, int limit)`
`Collection<DoubleVectorValueObject>`	ProcessedExpressionDataVectorServiceImpl.`getRandomProcessedDataArrays(ExpressionExperiment ee, int limit)`
`Map<Gene,Collection<Double>>`	ProcessedExpressionDataVectorDao.`getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)`
`Map<Gene,Collection<Double>>`	ProcessedExpressionDataVectorDaoImpl.`getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)`
`void`	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)`	Replace the processed vectors of a EE with the given vectors.
`int`	ProcessedExpressionDataVectorServiceImpl.`replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)`
`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<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 ExpressionExperiment
Modifier and Type	Method	Description
`ExpressionExperiment`	BioMaterialDao.`getExpressionExperiment(Long bioMaterialId)`
`ExpressionExperiment`	BioMaterialDaoImpl.`getExpressionExperiment(Long bioMaterialId)`
`ExpressionExperiment`	BioMaterialService.`getExpressionExperiment(Long id)`
`ExpressionExperiment`	BioMaterialServiceImpl.`getExpressionExperiment(Long id)`

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.`findByBioMaterial(BioMaterial bm)`
`ExpressionExperiment`	ExpressionExperimentDaoImpl.`findByBioMaterial(BioMaterial bm)`
`ExpressionExperiment`	ExpressionExperimentService.`findByBioMaterial(BioMaterial bm)`
`ExpressionExperiment`	ExpressionExperimentServiceImpl.`findByBioMaterial(BioMaterial bm)`
`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`	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`	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)`	A lightweight version of `ExpressionExperimentService.loadAndThawWithRefreshCacheMode(Long)` which thaws as per `ExpressionExperimentService.thawLite(ExpressionExperiment)`.
`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.`loadAndThawWithRefreshCacheMode(Long id)`	Load an experiment without cache and thaw it as per `ExpressionExperimentService.thaw(ExpressionExperiment)` with `CacheMode.REFRESH`.
`ExpressionExperiment`	ExpressionExperimentServiceImpl.`loadAndThawWithRefreshCacheMode(Long id)`
`ExpressionExperiment`	ExpressionExperimentService.`loadReference(Long id)`
`ExpressionExperiment`	ExpressionExperimentServiceImpl.`loadReference(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`	ExpressionExperimentService.`thaw(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentServiceImpl.`thaw(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentService.`thawBioAssays(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentServiceImpl.`thawBioAssays(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentService.`thawLite(ExpressionExperiment expressionExperiment)`	Partially thaw the expression experiment given - do not thaw the raw data.
`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(Long bibRefID)`
`Collection<ExpressionExperiment>`	ExpressionExperimentDaoImpl.`findByBibliographicReference(Long bibRefID)`
`Collection<ExpressionExperiment>`	ExpressionExperimentService.`findByBibliographicReference(BibliographicReference bibRef)`
`Collection<ExpressionExperiment>`	ExpressionExperimentServiceImpl.`findByBibliographicReference(BibliographicReference bibRef)`
`Map<ExpressionExperiment,BioMaterial>`	ExpressionExperimentDao.`findByBioMaterials(Collection<BioMaterial> bms)`
`Map<ExpressionExperiment,BioMaterial>`	ExpressionExperimentDaoImpl.`findByBioMaterials(Collection<BioMaterial> bms)`
`Map<ExpressionExperiment,BioMaterial>`	ExpressionExperimentService.`findByBioMaterials(Collection<BioMaterial> bioMaterials)`
`Map<ExpressionExperiment,BioMaterial>`	ExpressionExperimentServiceImpl.`findByBioMaterials(Collection<BioMaterial> bioMaterials)`
`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)`
`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
`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)`
`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)`	Create processed data vectors
`int`	ExpressionExperimentDaoImpl.`createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)`
`void`	ExpressionExperimentService.`createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)`
`void`	ExpressionExperimentServiceImpl.`createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)`
`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)`
`Collection<BioAssayDimension>`	ExpressionExperimentDao.`getBioAssayDimensions(ExpressionExperiment expressionExperiment)`
`Collection<BioAssayDimension>`	ExpressionExperimentDaoImpl.`getBioAssayDimensions(ExpressionExperiment expressionExperiment)`
`Collection<BioAssayDimension>`	ExpressionExperimentService.`getBioAssayDimensions(ExpressionExperiment expressionExperiment)`
`Collection<BioAssayDimension>`	ExpressionExperimentServiceImpl.`getBioAssayDimensions(ExpressionExperiment expressionExperiment)`
`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)`
`long`	ExpressionExperimentDao.`getDesignElementDataVectorCount(ExpressionExperiment ee)`
`long`	ExpressionExperimentDaoImpl.`getDesignElementDataVectorCount(ExpressionExperiment ee)`
`long`	ExpressionExperimentService.`getDesignElementDataVectorCount(ExpressionExperiment ee)`
`long`	ExpressionExperimentServiceImpl.`getDesignElementDataVectorCount(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)`
`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)`
`QuantitationType`	ExpressionExperimentDao.`getPreferredQuantitationType(ExpressionExperiment ee)`	Obtain the preferred quantitation type, if available.
`QuantitationType`	ExpressionExperimentDaoImpl.`getPreferredQuantitationType(ExpressionExperiment ee)`
`QuantitationType`	ExpressionExperimentService.`getPreferredQuantitationType(ExpressionExperiment ee)`	Iterates over the quantitation types for a given expression experiment and returns the preferred quantitation types.
`QuantitationType`	ExpressionExperimentServiceImpl.`getPreferredQuantitationType(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>`	ExpressionExperimentDao.`getQuantitationTypes(ExpressionExperiment expressionExperiment)`
`Collection<QuantitationType>`	ExpressionExperimentDaoImpl.`getQuantitationTypes(ExpressionExperiment expressionExperiment)`
`Collection<QuantitationType>`	ExpressionExperimentService.`getQuantitationTypes(ExpressionExperiment expressionExperiment)`
`Collection<QuantitationType>`	ExpressionExperimentServiceImpl.`getQuantitationTypes(ExpressionExperiment expressionExperiment)`
`Collection<QuantitationTypeValueObject>`	ExpressionExperimentService.`getQuantitationTypeValueObjects(ExpressionExperiment expressionExperiment)`	Load all `QuantitationType` associated to an expression experiment as VOs.
`Collection<QuantitationTypeValueObject>`	ExpressionExperimentServiceImpl.`getQuantitationTypeValueObjects(ExpressionExperiment expressionExperiment)`
`Collection<ExpressionExperimentSubSet>`	ExpressionExperimentDao.`getSubSets(ExpressionExperiment expressionExperiment)`
`Collection<ExpressionExperimentSubSet>`	ExpressionExperimentDaoImpl.`getSubSets(ExpressionExperiment expressionExperiment)`
`Collection<ExpressionExperimentSubSet>`	ExpressionExperimentService.`getSubSets(ExpressionExperiment expressionExperiment)`
`Collection<ExpressionExperimentSubSet>`	ExpressionExperimentServiceImpl.`getSubSets(ExpressionExperiment expressionExperiment)`
`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)`
`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.`removeProcessedDataVectors(ExpressionExperiment ee)`	Remove processed data vectors.
`int`	ExpressionExperimentDaoImpl.`removeProcessedDataVectors(ExpressionExperiment ee)`
`int`	ExpressionExperimentService.`removeProcessedDataVectors(ExpressionExperiment ee)`
`int`	ExpressionExperimentServiceImpl.`removeProcessedDataVectors(ExpressionExperiment ee)`
`int`	ExpressionExperimentDao.`removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)`	Remove raw data vectors for a given quantitation type.
`int`	ExpressionExperimentDaoImpl.`removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)`
`int`	ExpressionExperimentService.`removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)`
`int`	ExpressionExperimentServiceImpl.`removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)`
`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)`
`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)`
`void`	ExpressionExperimentDao.`thaw(ExpressionExperiment expressionExperiment)`
`void`	ExpressionExperimentDaoImpl.`thaw(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentService.`thaw(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentServiceImpl.`thaw(ExpressionExperiment expressionExperiment)`
`void`	ExpressionExperimentDao.`thawBioAssays(ExpressionExperiment expressionExperiment)`
`void`	ExpressionExperimentDaoImpl.`thawBioAssays(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentService.`thawBioAssays(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentServiceImpl.`thawBioAssays(ExpressionExperiment expressionExperiment)`
`void`	ExpressionExperimentDao.`thawForFrontEnd(ExpressionExperiment expressionExperiment)`
`void`	ExpressionExperimentDaoImpl.`thawForFrontEnd(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentService.`thawLite(ExpressionExperiment expressionExperiment)`	Partially thaw the expression experiment given - do not thaw the raw data.
`ExpressionExperiment`	ExpressionExperimentServiceImpl.`thawLite(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentService.`thawLiter(ExpressionExperiment expressionExperiment)`
`ExpressionExperiment`	ExpressionExperimentServiceImpl.`thawLiter(ExpressionExperiment expressionExperiment)`
`void`	ExpressionExperimentDao.`thawWithoutVectors(ExpressionExperiment expressionExperiment)`
`void`	ExpressionExperimentDaoImpl.`thawWithoutVectors(ExpressionExperiment ee)`
`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)`

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
`static Collection<ArrayDesign>`	CommonQueries.`getArrayDesignsUsed(ExpressionExperiment ee, Session session)`

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.
`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, Class<? extends DesignElementDataVector> vectorType)`

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 Collection<DesignMatrixRowValueObject>`	DesignMatrixRowValueObject.Factory.`getDesignMatrix(ExpressionExperiment expressionExperiment, boolean removeBatchFactor, boolean removeContinuous)`
`String`	ExpressionExperimentController.`getQCTagHTML(ExpressionExperiment ee)`	Used to include the html for the qc table in an ext panel (without using a tag) (This method should probably be in a service?)
`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

Uses of ExpressionExperiment in ubic.gemma.web.util

Methods in ubic.gemma.web.util with parameters of type ExpressionExperiment
Modifier and Type	Method	Description
`static String`	AnchorTagUtil.`getExpressionExperimentLink(ExpressionExperiment ee, String link, javax.servlet.ServletContext servletContext)`
`static String`	AnchorTagUtil.`getExpressionExperimentUrl(ExpressionExperiment ee, javax.servlet.ServletContext servletContext)`

Uses of Classubic.gemma.model.expression.experiment.ExpressionExperiment

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

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

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

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

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

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

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

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

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

Uses of ExpressionExperiment in ubic.gemma.core.apps

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

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

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

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

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

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

Uses of ExpressionExperiment in ubic.gemma.core.search

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

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

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

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

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

Uses of ExpressionExperiment in ubic.gemma.core.visualization

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

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

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

Uses of ExpressionExperiment in ubic.gemma.persistence.persister

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

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

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

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

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

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

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

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

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

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

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

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

Uses of ExpressionExperiment in ubic.gemma.persistence.util

Uses of ExpressionExperiment in ubic.gemma.rest

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

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

Uses of ExpressionExperiment in ubic.gemma.web.util

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