Uses of Class
ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix

Packages that use ExpressionDataDoubleMatrix

Package	Description
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.convert	Convert data from one QuantitationType to another.
ubic.gemma.core.analysis.preprocess.detect	This package contains classes for detecting and linting expression data.
ubic.gemma.core.analysis.preprocess.filter	This package contains classes for filtering expression data.
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.service
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.

Uses of ExpressionDataDoubleMatrix in ubic.gemma.core.analysis.expression.coexpression.links

Methods in ubic.gemma.core.analysis.expression.coexpression.links that return ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	LinkAnalysis.getDataMatrix()

Methods in ubic.gemma.core.analysis.expression.coexpression.links with parameters of type ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
void	LinkAnalysis.setDataMatrix(ExpressionDataDoubleMatrix paraDataMatrix)

Constructors in ubic.gemma.core.analysis.expression.coexpression.links with parameters of type ExpressionDataDoubleMatrix

Modifier	Constructor	Description
	PearsonMetrics(ExpressionDataDoubleMatrix dataMatrix)
	PearsonMetrics(ExpressionDataDoubleMatrix dataMatrix, double tmts)
	SpearmanMetrics(ExpressionDataDoubleMatrix dataMatrix)
	SpearmanMetrics(ExpressionDataDoubleMatrix dataMatrix, double tmts)

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

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

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	DifferentialExpressionAnalysisFilter.filter(ExpressionDataDoubleMatrix dataMatrix)

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

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	DifferentialExpressionAnalysisFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
Collection<DifferentialExpressionAnalysis>	DiffExAnalyzer.run(ExpressionExperiment expressionExperiment, Map<FactorValue,ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset with a pre-existing subset structure.
Collection<DifferentialExpressionAnalysis>	DiffExAnalyzer.run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset.
DifferentialExpressionAnalysis	DiffExAnalyzer.run(ExpressionExperimentSubSet subset, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a subset.
Collection<DifferentialExpressionAnalysis>	LinearModelAnalyzer.run(ExpressionExperiment ee, Map<FactorValue,ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	LinearModelAnalyzer.run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	I apologize for this being so complicated.
DifferentialExpressionAnalysis	LinearModelAnalyzer.run(ExpressionExperimentSubSet subset, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)

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

Methods in ubic.gemma.core.analysis.preprocess that return ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	MeanVarianceServiceHelper.getIntensities(ExpressionExperiment ee)

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

Methods in ubic.gemma.core.analysis.preprocess.batcheffects that return ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionService.comBat(ExpressionExperiment ee)	Run ComBat using default settings (parametric)
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionService.comBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix mat)	Run ComBat with a specific data matrix.
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionServiceImpl.comBat(ExpressionExperiment ee)
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionServiceImpl.comBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix originalDataMatrix)
static ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionServiceImpl.removeOutliers(ExpressionDataDoubleMatrix originalDataMatrix, ExpressionExperiment ee)	Remove outlier samples from the data matrix, based on outliers that were flagged in the experiment (not just candidate outliers)

Methods in ubic.gemma.core.analysis.preprocess.batcheffects with parameters of type ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionService.comBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix mat)	Run ComBat with a specific data matrix.
ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionServiceImpl.comBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix originalDataMatrix)
static ExpressionDataDoubleMatrix	ExpressionExperimentBatchCorrectionServiceImpl.removeOutliers(ExpressionDataDoubleMatrix originalDataMatrix, ExpressionExperiment ee)	Remove outlier samples from the data matrix, based on outliers that were flagged in the experiment (not just candidate outliers)

Uses of ExpressionDataDoubleMatrix in ubic.gemma.core.analysis.preprocess.convert

Methods in ubic.gemma.core.analysis.preprocess.convert that return ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
static ExpressionDataDoubleMatrix	QuantitationTypeConversionUtils.ensureLog2Scale(ExpressionDataDoubleMatrix expressionData)
static ExpressionDataDoubleMatrix	QuantitationTypeConversionUtils.ensureLog2Scale(ExpressionDataDoubleMatrix dmatrix, boolean ignoreQuantitationMismatch)	Ensures that the given matrix is on a Log2 scale.

Methods in ubic.gemma.core.analysis.preprocess.convert with parameters of type ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
static ExpressionDataDoubleMatrix	QuantitationTypeConversionUtils.ensureLog2Scale(ExpressionDataDoubleMatrix expressionData)
static ExpressionDataDoubleMatrix	QuantitationTypeConversionUtils.ensureLog2Scale(ExpressionDataDoubleMatrix dmatrix, boolean ignoreQuantitationMismatch)	Ensures that the given matrix is on a Log2 scale.

Uses of ExpressionDataDoubleMatrix in ubic.gemma.core.analysis.preprocess.detect

Methods in ubic.gemma.core.analysis.preprocess.detect with parameters of type ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
static void	QuantitationTypeDetectionUtils.detectSuspiciousValues(ExpressionDataDoubleMatrix a, QuantitationType qt)	Detect suspicious values for a given quantitation type.

Uses of ExpressionDataDoubleMatrix in ubic.gemma.core.analysis.preprocess.filter

Methods in ubic.gemma.core.analysis.preprocess.filter that return ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	AffyProbeNameFilter.filter(ExpressionDataDoubleMatrix data)
ExpressionDataDoubleMatrix	ExpressionExperimentFilter.filter(ExpressionDataDoubleMatrix matrix)
ExpressionDataDoubleMatrix	ExpressionExperimentFilter.filter(ExpressionDataDoubleMatrix eeDoubleMatrix, FilterResult result)
ExpressionDataDoubleMatrix	LowVarianceFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	RepetitiveValuesFilter.filter(ExpressionDataDoubleMatrix dmatrix)	We do this second because doing it first causes some kind of subtle problem ...
ExpressionDataDoubleMatrix	RowMissingValueFilter.filter(ExpressionDataDoubleMatrix data)
ExpressionDataDoubleMatrix	RowsWithSequencesFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	TooFewDistinctValuesFilter.filter(ExpressionDataDoubleMatrix matrix)
ExpressionDataDoubleMatrix	ZeroVarianceFilter.filter(ExpressionDataDoubleMatrix matrix)

Methods in ubic.gemma.core.analysis.preprocess.filter with parameters of type ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	AffyProbeNameFilter.filter(ExpressionDataDoubleMatrix data)
ExpressionDataDoubleMatrix	ExpressionExperimentFilter.filter(ExpressionDataDoubleMatrix matrix)
ExpressionDataDoubleMatrix	ExpressionExperimentFilter.filter(ExpressionDataDoubleMatrix eeDoubleMatrix, FilterResult result)
ExpressionDataDoubleMatrix	LowVarianceFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	RepetitiveValuesFilter.filter(ExpressionDataDoubleMatrix dmatrix)	We do this second because doing it first causes some kind of subtle problem ...
ExpressionDataDoubleMatrix	RowMissingValueFilter.filter(ExpressionDataDoubleMatrix data)
ExpressionDataDoubleMatrix	RowsWithSequencesFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	TooFewDistinctValuesFilter.filter(ExpressionDataDoubleMatrix matrix)
ExpressionDataDoubleMatrix	ZeroVarianceFilter.filter(ExpressionDataDoubleMatrix matrix)

Uses of ExpressionDataDoubleMatrix in ubic.gemma.core.analysis.preprocess.svd

Methods in ubic.gemma.core.analysis.preprocess.svd that return ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	ExpressionDataSVD.equalize()	Implements the method described in the SPELL paper, alternative interpretation as related by Q.
ExpressionDataDoubleMatrix	ExpressionDataSVD.removeHighestComponents(int numComponentsToRemove)	Provide a reconstructed matrix removing the first N components (the most significant ones).
ExpressionDataDoubleMatrix	ExpressionDataSVD.uMatrixAsExpressionData()
ExpressionDataDoubleMatrix	ExpressionDataSVD.winnow(double thresholdQuantile)	Implements method described in Skillicorn et al., "Strategies for winnowing microarray data" (also section 3.5.5 of his book)

Constructors in ubic.gemma.core.analysis.preprocess.svd with parameters of type ExpressionDataDoubleMatrix

Modifier	Constructor	Description
	ExpressionDataSVD(ExpressionDataDoubleMatrix expressionData)	Does normalization.
	ExpressionDataSVD(ExpressionDataDoubleMatrix expressionData, boolean normalizeMatrix)

Uses of ExpressionDataDoubleMatrix in ubic.gemma.core.analysis.service

Methods in ubic.gemma.core.analysis.service that return ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors, ArrayDesign arrayDesign, FilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, FilterConfig filterConfig, boolean logTransform)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors, ArrayDesign arrayDesign, FilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, FilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getProcessedExpressionDataMatrix(ExpressionExperiment ee)	Obtain the processed expression data matrix for a given experiment.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getProcessedExpressionDataMatrix(ExpressionExperiment ee, boolean thawAssays)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getProcessedExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getProcessedExpressionDataMatrix(ExpressionExperiment ee)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getProcessedExpressionDataMatrix(ExpressionExperiment ee, boolean thawAssays)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getProcessedExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getRawExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain a raw expression data matrix for a given quantitation type
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getRawExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)

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

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

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	TwoChannelExpressionDataMatrixBuilder.getBackgroundChannelA()
ExpressionDataDoubleMatrix	TwoChannelExpressionDataMatrixBuilder.getBackgroundChannelB()
ExpressionDataDoubleMatrix	TwoChannelExpressionDataMatrixBuilder.getBkgSubChannelA()
ExpressionDataDoubleMatrix	TwoChannelExpressionDataMatrixBuilder.getIntensity()
ExpressionDataDoubleMatrix	TwoChannelExpressionDataMatrixBuilder.getPreferredData()
ExpressionDataDoubleMatrix	TwoChannelExpressionDataMatrixBuilder.getProcessedData()
ExpressionDataDoubleMatrix	TwoChannelExpressionDataMatrixBuilder.getSignalChannelA()
ExpressionDataDoubleMatrix	TwoChannelExpressionDataMatrixBuilder.getSignalChannelB()
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.sliceRows(List<CompositeSequence> designElements)

Methods in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
void	TwoChannelExpressionDataMatrixBuilder.addMatrices(ExpressionDataDoubleMatrix a, ExpressionDataDoubleMatrix b)	Add two matrices.
static void	TwoChannelExpressionDataMatrixBuilder.logTransformMatrix(ExpressionDataDoubleMatrix matrix)	Log-transform the values in the matrix (base 2).
void	TwoChannelExpressionDataMatrixBuilder.scalarDivideMatrix(ExpressionDataDoubleMatrix matrix, double dividend)	Divide all values by the dividend

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

Modifier	Constructor	Description
	ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<BioMaterial> columnsToUse, BioAssayDimension reorderedDim)	Create a matrix based on another one's selected columns.
	ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix dmatrix, DoubleMatrix<CompositeSequence,BioMaterial> copiedMatrix)
	ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix, Collection<QuantitationType> quantitationTypes)	Create a data matrix like sourceMatrix but use the values and quantitations from dataMatrix.

Uses of ExpressionDataDoubleMatrix in ubic.gemma.core.loader.expression

Methods in ubic.gemma.core.loader.expression with parameters of type ExpressionDataDoubleMatrix

Modifier and Type	Method	Description
void	DataUpdater.addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	DataUpdaterImpl.addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)	Generic but in practice used for RNA-seq.
void	DataUpdater.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	DataUpdaterImpl.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)	Replace the data associated with the experiment (or add it if there is none).