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

Packages that use DifferentialExpressionAnalysis

Package	Description
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.core.analysis.expression.diff

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

Modifier and Type	Method	Description
DifferentialExpressionAnalysis	AnalysisSelectionAndExecutionService.analyze(ExpressionExperimentSubSet subset, DifferentialExpressionAnalysisConfig config)
DifferentialExpressionAnalysis	AnalysisSelectionAndExecutionServiceImpl.analyze(ExpressionExperimentSubSet subset, DifferentialExpressionAnalysisConfig config)
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, DifferentialExpressionAnalysisConfig config)	Note that normally when we run a subset analysis, the subsetting is done internally, so we pass in the expression experiment, not the subset.
DifferentialExpressionAnalysis	LinearModelAnalyzer.run(ExpressionExperimentSubSet subset, 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>	AnalysisSelectionAndExecutionService.analyze(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	AnalysisSelectionAndExecutionServiceImpl.analyze(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.getAnalyses(ExpressionExperiment expressionExperiment)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.getAnalyses(ExpressionExperiment expressionExperiment)
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)

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)	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)
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 copyMe, boolean persist)	Redo
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis copyMe, boolean persist)

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
void	ExpressionDataFileService.deleteDiffExArchiveFile(DifferentialExpressionAnalysis analysis)
void	ExpressionDataFileServiceImpl.deleteDiffExArchiveFile(DifferentialExpressionAnalysis analysis)
void	ExpressionDataFileService.writeDiffExArchiveFile(BioAssaySet ee, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)	Writes to the configured gemma.appdata.home The file created is a zip archive containing at least two files.
void	ExpressionDataFileServiceImpl.writeDiffExArchiveFile(BioAssaySet experimentAnalyzed, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)

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

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()

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

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.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.find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByExperiment(BioAssaySet experiment)
Map<Long,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.findByExperimentIds(Collection<Long> investigationIds)
Map<Long,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.findByExperimentIds(Collection<Long> investigationIds)
Map<Long,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperimentIds(Collection<Long> experimentIds)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperiments(Collection<BioAssaySet> experiments)
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>	DifferentialExpressionAnalysisServiceImpl.findByName(String name)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.findByTaxon(Taxon taxon)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByTaxon(Taxon taxon)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.getAnalyses(BioAssaySet expressionExperiment)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.getAnalyses(BioAssaySet expressionExperiment)
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)