Uses of Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet (Gemma 1.31.2 API)

Packages that use ExpressionExperimentSubSet
Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util

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.model.expression.bioAssayData

Constructors in ubic.gemma.model.expression.bioAssayData with parameters of type ExpressionExperimentSubSet
Constructor	Description
`DoubleVectorValueObject(ExpressionExperimentSubSet bioassaySet, DoubleVectorValueObject vec, BioAssayDimensionValueObject bad)`	Create a vector that is a slice of another one.

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)`