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)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisConfig.toAnalysis()

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. ex. analysis archive file for a given analysis.
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()
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	DifferentialExpressionAnalysisService.create(DifferentialExpressionAnalysis analysis)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisService.findByExperimentAnalyzedAndId(ExpressionExperiment expressionExperiment, Long analysisId, boolean includeSubSets)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisServiceImpl.findByExperimentAnalyzedAndId(ExpressionExperiment expressionExperiment, Long analysisId, boolean includeSubSets)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisDao.findByExperimentAndAnalysisId(ExpressionExperiment experimentAnalyzed, Long analysisId, boolean includeSubSets)	Find an analysis for the given experiment and identifier.
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>	DifferentialExpressionAnalysisService.findByExperiment(ExpressionExperiment experimentAnalyzed, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByExperiment(ExpressionExperiment experiment, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByExperimentAnalyzed(BioAssaySet experimentAnalyzed)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByExperimentAnalyzed(ExpressionExperiment experiment, boolean includeSubSets)	Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().
Map<Long,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.findByExperimentAnalyzedId(Collection<Long> experimentAnalyzedId)
Map<Long,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.findByExperimentIds(Collection<Long> investigationIds)
Map<Long,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperimentIds(Collection<Long> experimentIds)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.findByExperiments(Collection<ExpressionExperiment> investigations, boolean includeSubSets)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.findByExperimentsAnalyzed(Collection<ExpressionExperiment> experiments, boolean includeSubSets)	Given a collection of experiments returns a Map of Analysis --> collection of Experiments The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with
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)
DifferentialExpressionAnalysis	DifferentialExpressionAnalysisService.create(DifferentialExpressionAnalysis analysis)
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)
void	DifferentialExpressionAnalysisService.update(DifferentialExpressionAnalysis o)

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)