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

Packages that use ExpressionExperimentSubSet

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest

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

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

Modifier and Type	Method	Description
DifferentialExpressionAnalysis	AnalysisSelectionAndExecutionService.analyze(ExpressionExperimentSubSet subset, DifferentialExpressionAnalysisConfig config)
DifferentialExpressionAnalysis	AnalysisSelectionAndExecutionServiceImpl.analyze(ExpressionExperimentSubSet subset, DifferentialExpressionAnalysisConfig config)
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)

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

Methods in ubic.gemma.core.analysis.preprocess.batcheffects that return types with arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
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)

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

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

Modifier and Type	Method	Description
SlicedDoubleVectorValueObject	DoubleVectorValueObject.slice(ExpressionExperimentSubSet subset, BioAssayDimensionValueObject bad)	Crate a vector that is a slice of this one.

Constructors in ubic.gemma.model.expression.bioAssayData with parameters of type ExpressionExperimentSubSet

Constructor	Description
SlicedDoubleVectorValueObject(DoubleVectorValueObject vec, ExpressionExperimentSubSet bioassaySet, BioAssayDimensionValueObject slicedBad)	Constructor for creating a slice.

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

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

Modifier and Type	Method	Description
static ExpressionExperimentSubSet	ExpressionExperimentSubSet.Factory.newInstance()

Constructors in ubic.gemma.model.expression.experiment with parameters of type ExpressionExperimentSubSet

Constructor	Description
ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet ees)

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

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

Modifier and Type	Method	Description
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.create(ExpressionExperimentSubSet expressionExperimentSubSet)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDao.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDaoImpl.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDao.findOrCreate(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.findOrCreate(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.load(Long id)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDao.getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDaoImpl.getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetService.loadAll()

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.create(ExpressionExperimentSubSet expressionExperimentSubSet)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDao.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDaoImpl.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDao.findOrCreate(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.findOrCreate(ExpressionExperimentSubSet entity)
Collection<FactorValue>	ExpressionExperimentSubSetDao.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetDaoImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetService.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetServiceImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
void	ExpressionExperimentSubSetService.remove(ExpressionExperimentSubSet entity)	Deletes an experiment subset and all of its associated DifferentialExpressionAnalysis objects.
void	ExpressionExperimentSubSetServiceImpl.remove(ExpressionExperimentSubSet subset)	doesn't include removal of sample coexpression matrices, PCA, probe2probe coexpression links, or adjusting experiment set members

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
void	ExpressionExperimentSubSetServiceImpl.remove(Collection<ExpressionExperimentSubSet> entities)

Uses of ExpressionExperimentSubSet in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
static void	BusinessKey.checkKey(ExpressionExperimentSubSet entity)
static void	BusinessKey.createQueryObject(Criteria queryObject, ExpressionExperimentSubSet entity)

Uses of ExpressionExperimentSubSet in ubic.gemma.rest

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

Constructor	Description
BatchInformationValueObject(BatchEffectType batchEffectType, BatchEffectDetails batchEffectDetails, List<BatchConfound> batchConfound, Map<ExpressionExperimentSubSet,List<BatchConfound>> subsetBatchConfounds)