Uses of Class
ubic.gemma.model.expression.bioAssayData.BioAssayDimension
-
-
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 occursCollection<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)
-