Uses of Class
ubic.gemma.model.expression.bioAssayData.BioAssayDimension

Packages that use BioAssayDimension

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess
ubic.gemma.core.datastructure.matrix
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.expression.bioAssayData
ubic.gemma.persistence.service.analysis.expression.pca
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment

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

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

Modifier and Type	Method	Description
static BioAssayDimension	LinearModelAnalyzer.createBADMap(List<BioMaterial> columnsToUse)	This bioAssayDimension shouldn't get persisted; it is only for dealing with subset diff ex.

Uses of BioAssayDimension in ubic.gemma.core.analysis.preprocess

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

Modifier and Type	Method	Description
List<BioAssayDimension>	ExpressionDataMatrixBuilder.getBioAssayDimensions()

Uses of BioAssayDimension in ubic.gemma.core.datastructure.matrix

Methods in ubic.gemma.core.datastructure.matrix that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	BaseExpressionDataMatrix.getBestBioAssayDimension()
BioAssayDimension	ExpressionDataMatrix.getBestBioAssayDimension()
BioAssayDimension	BaseExpressionDataMatrix.getBioAssayDimension(CompositeSequence designElement)
BioAssayDimension	ExpressionDataMatrix.getBioAssayDimension(CompositeSequence designElement)	Produce a BioAssayDimension representing the matrix columns for a specific row.

Constructors in ubic.gemma.core.datastructure.matrix with parameters of type BioAssayDimension

Constructor	Description
EmptyExpressionMatrix(BioAssayDimension ba)
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<BioMaterial> columnsToUse, BioAssayDimension reorderedDim)	Create a matrix based on another one's selected columns.

Constructor parameters in ubic.gemma.core.datastructure.matrix with type arguments of type BioAssayDimension

Constructor	Description
EmptyExpressionMatrix(Collection<BioAssayDimension> dims)

Uses of BioAssayDimension in ubic.gemma.model.analysis.expression.coexpression

Methods in ubic.gemma.model.analysis.expression.coexpression that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	SampleCoexpressionMatrix.getBioAssayDimension()

Methods in ubic.gemma.model.analysis.expression.coexpression with parameters of type BioAssayDimension

Modifier and Type	Method	Description
void	SampleCoexpressionMatrix.setBioAssayDimension(BioAssayDimension bioAssayDimension)

Constructors in ubic.gemma.model.analysis.expression.coexpression with parameters of type BioAssayDimension

Constructor	Description
SampleCoexpressionMatrix(BioAssayDimension bioAssayDimension, byte[] coexpressionMatrix)

Uses of BioAssayDimension in ubic.gemma.model.analysis.expression.pca

Methods in ubic.gemma.model.analysis.expression.pca that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	PrincipalComponentAnalysis.getBioAssayDimension()

Methods in ubic.gemma.model.analysis.expression.pca with parameters of type BioAssayDimension

Modifier and Type	Method	Description
void	PrincipalComponentAnalysis.setBioAssayDimension(BioAssayDimension bioAssayDimension)

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

Methods in ubic.gemma.model.expression.bioAssayData that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	DesignElementDataVector.getBioAssayDimension()
static BioAssayDimension	BioAssayDimension.Factory.newInstance()
static BioAssayDimension	BioAssayDimension.Factory.newInstance(String name, String description, List<BioAssay> bioAssays)

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

Modifier and Type	Method	Description
void	DesignElementDataVector.setBioAssayDimension(BioAssayDimension bioAssayDimension)

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

Constructor	Description
BioAssayDimensionValueObject(BioAssayDimension entity)
DoubleVectorValueObject(DesignElementDataVector dedv, BioAssayDimensionValueObject vectorsBadVo, Collection<Long> genes, BioAssayDimension dimToMatch)	Create a vector where we expect to have to create one or more gaps to match other vectors, defined by dimToMatch.

Uses of BioAssayDimension in ubic.gemma.persistence.service.analysis.expression.pca

Methods in ubic.gemma.persistence.service.analysis.expression.pca with parameters of type BioAssayDimension

Modifier and Type	Method	Description
PrincipalComponentAnalysis	PrincipalComponentAnalysisService.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence,Integer> u, double[] eigenvalues, DoubleMatrix<Integer,BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)
PrincipalComponentAnalysis	PrincipalComponentAnalysisServiceImpl.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence,Integer> u, double[] eigenvalues, DoubleMatrix<Integer,BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)

Uses of BioAssayDimension in ubic.gemma.persistence.service.expression.bioAssay

Methods in ubic.gemma.persistence.service.expression.bioAssay that return types with arguments of type BioAssayDimension

Modifier and Type	Method	Description
Collection<BioAssayDimension>	BioAssayDao.findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssayDimension>	BioAssayDaoImpl.findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssayDimension>	BioAssayService.findBioAssayDimensions(BioAssay bioAssay)	Locate all BioAssayDimensions in which the selected BioAssay occurs
Collection<BioAssayDimension>	BioAssayServiceImpl.findBioAssayDimensions(BioAssay bioAssay)

Uses of BioAssayDimension in ubic.gemma.persistence.service.expression.bioAssayData

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	BioAssayDimensionService.create(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionDaoImpl.find(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.findOrCreate(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.thaw(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionServiceImpl.thaw(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.thawLite(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionServiceImpl.thawLite(BioAssayDimension bioAssayDimension)

Methods in ubic.gemma.persistence.service.expression.bioAssayData with parameters of type BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	BioAssayDimensionService.create(BioAssayDimension bioAssayDimension)
protected BioAssayDimensionValueObject	BioAssayDimensionDaoImpl.doLoadValueObject(BioAssayDimension entity)
Collection<T>	AbstractDesignElementDataVectorDao.find(BioAssayDimension bioAssayDimension)
Collection<T>	AbstractDesignElementDataVectorService.find(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionDaoImpl.find(BioAssayDimension bioAssayDimension)
Collection<T>	DesignElementDataVectorDao.find(BioAssayDimension bioAssayDimension)
Collection<T>	AbstractDesignElementDataVectorService.findAndThaw(BioAssayDimension bioAssayDimension)
Collection<DesignElementDataVector>	RawAndProcessedExpressionDataVectorServiceImpl.findAndThaw(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.findOrCreate(BioAssayDimension bioAssayDimension)
void	BioAssayDimensionService.remove(BioAssayDimension bioAssayDimension)
void	BioAssayDimensionDao.thaw(BioAssayDimension bioAssayDimension)
void	BioAssayDimensionDaoImpl.thaw(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.thaw(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionServiceImpl.thaw(BioAssayDimension bioAssayDimension)
void	BioAssayDimensionDao.thawLite(BioAssayDimension bioAssayDimension)
void	BioAssayDimensionDaoImpl.thawLite(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.thawLite(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionServiceImpl.thawLite(BioAssayDimension bioAssayDimension)

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

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

Modifier and Type	Method	Description
Collection<BioAssayDimension>	ExpressionExperimentDao.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentService.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentServiceImpl.getBioAssayDimensions(ExpressionExperiment expressionExperiment)