Uses of Class
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis

Packages that use DifferentialExpressionAnalysis

Package	Description
ubic.gemma.cli.util
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.service
ubic.gemma.core.tasks.analysis.diffex
ubic.gemma.model.analysis.expression.diff
ubic.gemma.persistence.service.analysis.expression.diff

Uses of DifferentialExpressionAnalysis in ubic.gemma.cli.util

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

Modifier and Type	Method	Description
DifferentialExpressionAnalysis	EntityLocator.locateDiffExAnalysis(ExpressionExperiment ee, String analysisIdentifier)
DifferentialExpressionAnalysis	EntityLocatorImpl.locateDiffExAnalysis(ExpressionExperiment ee, String analysisIdentifier)

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

Methods in ubic.gemma.core.analysis.expression.diff that return DifferentialExpressionAnalysis

Modifier and Type	Method	Description
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.
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisHelperService.persistStub(DifferentialExpressionAnalysis entity)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisHelperServiceImpl.persistStub(DifferentialExpressionAnalysis entity)
DifferentialExpressionAnalysis	DiffExAnalyzer.run(ExpressionExperimentSubSet subset, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a subset.
DifferentialExpressionAnalysis	LinearModelAnalyzer.run(ExpressionExperimentSubSet subset, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)

Methods in ubic.gemma.core.analysis.expression.diff that return types with arguments of type DifferentialExpressionAnalysis

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.getAnalyses(ExpressionExperiment expressionExperiment)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.getAnalyses(ExpressionExperiment expressionExperiment)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> deas, DifferentialExpressionAnalysisConfig config, boolean ignoreFailingAnalyses)	Redo multiple analyses.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> deas, DifferentialExpressionAnalysisConfig config, boolean ignoreFailingAnalyses)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea)	Redo an analysis.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea, DifferentialExpressionAnalysisConfig config)	Redo an analysis.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	DiffExAnalyzer.run(ExpressionExperiment expressionExperiment, Map<FactorValue,ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset with a pre-existing subset structure.
Collection<DifferentialExpressionAnalysis>	DiffExAnalyzer.run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset.
Collection<DifferentialExpressionAnalysis>	LinearModelAnalyzer.run(ExpressionExperiment ee, Map<FactorValue,ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	LinearModelAnalyzer.run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	I apologize for this being so complicated.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)

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

Modifier and Type	Method	Description
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, DifferentialExpressionAnalysisConfig config)	Like redo, but we don't save the results, we just add the full set of results to the analysis given.
Collection<ExpressionAnalysisResultSet>	DifferentialExpressionAnalyzerServiceImpl.extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate, DifferentialExpressionAnalysisConfig baseConfig)
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.
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisHelperService.persistStub(DifferentialExpressionAnalysis entity)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisHelperServiceImpl.persistStub(DifferentialExpressionAnalysis entity)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea)	Redo an analysis.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea, DifferentialExpressionAnalysisConfig config)	Redo an analysis.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea, DifferentialExpressionAnalysisConfig config)

Method parameters in ubic.gemma.core.analysis.expression.diff with type arguments of type DifferentialExpressionAnalysis

Modifier and Type	Method	Description
int	DifferentialExpressionAnalyzerService.deleteAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> analysesToDelete)	Delete the specified differential expression analyses associated with the experiment.
int	DifferentialExpressionAnalyzerServiceImpl.deleteAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> analysesToDelete)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> deas, DifferentialExpressionAnalysisConfig config, boolean ignoreFailingAnalyses)	Redo multiple analyses.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> deas, DifferentialExpressionAnalysisConfig config, boolean ignoreFailingAnalyses)

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

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

Modifier and Type	Method	Description
boolean	ExpressionDataFileService.deleteDiffExArchiveFile(DifferentialExpressionAnalysis analysis)	Delete a diff.
boolean	ExpressionDataFileServiceImpl.deleteDiffExArchiveFile(DifferentialExpressionAnalysis analysis)
static String	ExpressionDataFileUtils.getDiffExArchiveFileName(DifferentialExpressionAnalysis diff)
void	DiffExAnalysisResultSetWriter.write(DifferentialExpressionAnalysis analysis, Map<CompositeSequence,String[]> geneAnnotations, DifferentialExpressionAnalysisConfig config, boolean hasSignificantBatchConfound, OutputStream stream)	Write a DifferentialExpressionAnalysis as a ZIP archive containing entries for the analysis and each result set.
void	ExpressionDataFileService.writeDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis analysis, OutputStream outputStream)	Write a differential expression analysis archive file for a given analysis to an output stream.
void	ExpressionDataFileServiceImpl.writeDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis analysis, OutputStream stream)
LockedPath	ExpressionDataFileService.writeOrLocateDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis analysis, boolean forceWrite)	Locate or create the differential expression archive file for a given analysis.
LockedPath	ExpressionDataFileServiceImpl.writeOrLocateDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis analysis, boolean forceCreate)

Method parameters in ubic.gemma.core.analysis.service with type arguments of type DifferentialExpressionAnalysis

Modifier and Type	Method	Description
Collection<Path>	ExpressionDataFileService.writeDiffExAnalysisArchiveFiles(Collection<DifferentialExpressionAnalysis> analyses, Path outputDir, boolean forceWrite)
Collection<Path>	ExpressionDataFileServiceImpl.writeDiffExAnalysisArchiveFiles(Collection<DifferentialExpressionAnalysis> analyses, Path outputDir, boolean forceWrite)

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

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

Modifier and Type	Method	Description
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisTaskCommand.getToRedo()
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisRemoveTaskCommand.getToRemove()

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

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisTaskCommand.setToRedo(DifferentialExpressionAnalysis toRedo)

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

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

Uses of DifferentialExpressionAnalysis in ubic.gemma.model.analysis.expression.diff

Methods in ubic.gemma.model.analysis.expression.diff that return DifferentialExpressionAnalysis

Modifier and Type	Method	Description
DifferentialExpressionAnalysis	ExpressionAnalysisResultSet.getAnalysis()
DifferentialExpressionAnalysis	ExpressionAnalysisResultSet.getSecurityOwner()
static DifferentialExpressionAnalysis	DifferentialExpressionAnalysis.Factory.newInstance()
static DifferentialExpressionAnalysis	RandomDifferentialExpressionAnalysisUtils.randomAnalysis(BioAssaySet experimentAnalyzed, ExperimentalDesign design, ArrayDesign platform)

Methods in ubic.gemma.model.analysis.expression.diff with parameters of type DifferentialExpressionAnalysis

Modifier and Type	Method	Description
static ExpressionAnalysisResultSet	ExpressionAnalysisResultSet.Factory.newInstance(Set<ExperimentalFactor> experimentalFactors, Integer numberOfProbesTested, Integer numberOfGenesTested, FactorValue baselineGroup, Set<DifferentialExpressionAnalysisResult> results, DifferentialExpressionAnalysis analysis, PvalueDistribution pvalueDistribution, Set<HitListSize> hitListSizes)
void	ExpressionAnalysisResultSet.setAnalysis(DifferentialExpressionAnalysis analysis)

Constructors in ubic.gemma.model.analysis.expression.diff with parameters of type DifferentialExpressionAnalysis

Modifier	Constructor	Description
	DifferentialExpressionAnalysisValueObject(DifferentialExpressionAnalysis analysis)	Does not populate the resultSets.

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

Methods in ubic.gemma.persistence.service.analysis.expression.diff that return DifferentialExpressionAnalysis

Modifier and Type	Method	Description
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisDao.findByExperimentAndAnalysisId(ExpressionExperiment experimentAnalyzed, boolean includeSubSets, Long analysisId)	Find an analysis for the given experiment and identifier.
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisService.findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisServiceImpl.findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisService.loadWithExperimentAnalyzed(Long id)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisServiceImpl.loadWithExperimentAnalyzed(Long id)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisService.thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisServiceImpl.thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisService.thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisServiceImpl.thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

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

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByExperiment(ExpressionExperiment experiment, boolean includeSubSets)	Find by associated ExpressionExperiment.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.findByExperiment(ExpressionExperiment experimentAnalyzed, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByExperiment(ExpressionExperiment experiment, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByExperimentAnalyzed(BioAssaySet experimentAnalyzed)	Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.findByExperimentIds(Collection<Long> experimentIds, boolean includeSubSets, Map<Long,Collection<Long>> arrayDesignUsed, Map<Long,Collection<FactorValue>> ee2fv)	Retrieve analysis for the given experiment or experiment subset IDs.
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)	Find by associated ExpressionExperiments.
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByFactor(ExperimentalFactor ef)	Retrieve analyses associated with the factor, either through the subset factor or as factors for result sets.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByFactors(Collection<ExperimentalFactor> experimentalFactors)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByName(String name)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.findByName(String name)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByName(String name)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)

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

Modifier and Type	Method	Description
boolean	DifferentialExpressionAnalysisService.canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
boolean	DifferentialExpressionAnalysisServiceImpl.canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
boolean	ExpressionAnalysisResultSetDao.canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
boolean	ExpressionAnalysisResultSetDaoImpl.canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
void	DifferentialExpressionAnalysisServiceImpl.remove(DifferentialExpressionAnalysis toDelete)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisService.thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisServiceImpl.thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisService.thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisServiceImpl.thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

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

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisServiceImpl.remove(Collection<DifferentialExpressionAnalysis> entities)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)