Uses of Class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix (Gemma 1.31.13 API)

Packages that use ExpressionDataDoubleMatrix
Package	Description
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.filter
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.service
ubic.gemma.core.datastructure.matrix
ubic.gemma.core.loader.expression
ubic.gemma.model.expression.experiment

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
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 with parameters of type ExpressionDataDoubleMatrix
Modifier and Type	Method	Description
`abstract Collection<DifferentialExpressionAnalysis>`	AbstractDifferentialExpressionAnalyzer.`run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)`
`Collection<DifferentialExpressionAnalysis>`	DiffExAnalyzer.`run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)`	Allows entry of modified data matrices into the workflow.
`Collection<DifferentialExpressionAnalysis>`	LinearModelAnalyzer.`run(ExpressionExperiment expressionExperiment, 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`	ExpressionDataMatrixBuilder.`getBackgroundChannelA()`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixBuilder.`getBackgroundChannelB()`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixBuilder.`getBkgSubChannelA()`
`ExpressionDataDoubleMatrix`	MeanVarianceServiceHelper.`getIntensities(ExpressionExperiment ee)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixBuilder.`getIntensity()`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixBuilder.`getPreferredData()`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixBuilder.`getProcessedData()`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixBuilder.`getSignalChannelA()`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixBuilder.`getSignalChannelB()`

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.filter

Methods in ubic.gemma.core.analysis.preprocess.filter that return ExpressionDataDoubleMatrix
Modifier and Type	Method	Description
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`doNothingFilter(ExpressionDataDoubleMatrix matrix)`
`ExpressionDataDoubleMatrix`	AffyProbeNameFilter.`filter(ExpressionDataDoubleMatrix data)`
`ExpressionDataDoubleMatrix`	RowLevelFilter.`filter(ExpressionDataDoubleMatrix data)`
`ExpressionDataDoubleMatrix`	RowMissingValueFilter.`filter(ExpressionDataDoubleMatrix data)`
`ExpressionDataDoubleMatrix`	RowsWithSequencesFilter.`filter(ExpressionDataDoubleMatrix dataMatrix)`
`ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors)`	Provides a ready-to-use expression data matrix that is transformed and filtered.
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`lowVarianceFilter(ExpressionDataDoubleMatrix matrix, int quantile)`	Remove rows that have a low variance, below the stated quantile
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`tooFewDistinctValues(ExpressionDataDoubleMatrix matrix, double threshold)`	Remove rows that have a low diversity of values (equality judged based on tolerancee set in RowLevelFilter).
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`tooFewDistinctValues(ExpressionDataDoubleMatrix matrix, double threshold, double tolerance)`
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`zeroVarianceFilter(ExpressionDataDoubleMatrix matrix)`	Remove rows that have a variance of zero (within a small constant)

Methods in ubic.gemma.core.analysis.preprocess.filter with parameters of type ExpressionDataDoubleMatrix
Modifier and Type	Method	Description
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`doNothingFilter(ExpressionDataDoubleMatrix matrix)`
`ExpressionDataDoubleMatrix`	AffyProbeNameFilter.`filter(ExpressionDataDoubleMatrix data)`
`ExpressionDataDoubleMatrix`	RowLevelFilter.`filter(ExpressionDataDoubleMatrix data)`
`ExpressionDataDoubleMatrix`	RowMissingValueFilter.`filter(ExpressionDataDoubleMatrix data)`
`ExpressionDataDoubleMatrix`	RowsWithSequencesFilter.`filter(ExpressionDataDoubleMatrix dataMatrix)`
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`lowVarianceFilter(ExpressionDataDoubleMatrix matrix, int quantile)`	Remove rows that have a low variance, below the stated quantile
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`tooFewDistinctValues(ExpressionDataDoubleMatrix matrix, double threshold)`	Remove rows that have a low diversity of values (equality judged based on tolerancee set in RowLevelFilter).
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`tooFewDistinctValues(ExpressionDataDoubleMatrix matrix, double threshold, double tolerance)`
`static ExpressionDataDoubleMatrix`	ExpressionExperimentFilter.`zeroVarianceFilter(ExpressionDataDoubleMatrix matrix)`	Remove rows that have a variance of zero (within a small constant)

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
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(String arrayDesignName, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixService.`getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig)`	Provide a filtered expression data matrix.
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixService.`getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)`	Provide a filtered expression data matrix.
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixServiceImpl.`getFilteredMatrix(String arrayDesignName, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixServiceImpl.`getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixServiceImpl.`getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixService.`getProcessedExpressionDataMatrix(ExpressionExperiment ee)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixServiceImpl.`getProcessedExpressionDataMatrix(ExpressionExperiment ee)`
`ExpressionDataDoubleMatrix`	ExpressionDataMatrixService.`getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)`	Obtain a raw expression data matrix for a given quantitation type
`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
`static ExpressionDataDoubleMatrix`	ExpressionDataDoubleMatrixUtil.`ensureLog2Scale(ExpressionDataDoubleMatrix expressionData)`
`static ExpressionDataDoubleMatrix`	ExpressionDataDoubleMatrixUtil.`ensureLog2Scale(ExpressionDataDoubleMatrix dmatrix, boolean ignoreQuantitationMismatch)`	Ensures that the given matrix is on a Log2 scale.
`static ExpressionDataDoubleMatrix`	ExpressionDataDoubleMatrixUtil.`filterAndLog2Transform(ExpressionDataDoubleMatrix dmatrix)`	Log2 transform if necessary, do any required filtering prior to analysis.

Methods in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionDataDoubleMatrix
Modifier and Type	Method	Description
`static void`	ExpressionDataDoubleMatrixUtil.`addMatrices(ExpressionDataDoubleMatrix a, ExpressionDataDoubleMatrix b)`	Add two matrices.
`static void`	ExpressionDataDoubleMatrixUtil.`detectSuspiciousValues(ExpressionDataDoubleMatrix a, QuantitationType qt)`	Detect suspicious values for a given quantitation type.
`static ExpressionDataDoubleMatrix`	ExpressionDataDoubleMatrixUtil.`ensureLog2Scale(ExpressionDataDoubleMatrix expressionData)`
`static ExpressionDataDoubleMatrix`	ExpressionDataDoubleMatrixUtil.`ensureLog2Scale(ExpressionDataDoubleMatrix dmatrix, boolean ignoreQuantitationMismatch)`	Ensures that the given matrix is on a Log2 scale.
`static ExpressionDataDoubleMatrix`	ExpressionDataDoubleMatrixUtil.`filterAndLog2Transform(ExpressionDataDoubleMatrix dmatrix)`	Log2 transform if necessary, do any required filtering prior to analysis.
`static QuantitationType`	ExpressionDataDoubleMatrixUtil.`inferQuantitationType(ExpressionDataDoubleMatrix expressionDataDoubleMatrix)`	Infer a `QuantitationType` from expression data.
`static void`	ExpressionDataDoubleMatrixUtil.`logTransformMatrix(ExpressionDataDoubleMatrix matrix)`	Log-transform the values in the matrix (base 2).
`static void`	ExpressionDataDoubleMatrixUtil.`maskMatrix(ExpressionDataDoubleMatrix matrix, ExpressionDataBooleanMatrix mask)`	Use the mask matrix to turn some values in a matrix to NaN.
`static void`	ExpressionDataDoubleMatrixUtil.`scalarDivideMatrix(ExpressionDataDoubleMatrix matrix, double dividend)`	Divide all values by the dividend
`static void`	ExpressionDataDoubleMatrixUtil.`subtractMatrices(ExpressionDataDoubleMatrix a, ExpressionDataDoubleMatrix b)`	Subtract two matrices.

Constructors in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionDataDoubleMatrix
Constructor	Description
`ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<BioMaterial> columnsToUse, BioAssayDimension reorderedDim)`	Create a matrix based on another one's selected columns.
`ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<CompositeSequence> rowsToUse)`	Create a matrix based on another one's selected rows.
`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).

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

Methods in ubic.gemma.model.expression.experiment with parameters of type ExpressionDataDoubleMatrix
Modifier and Type	Method	Description
`static List<BioMaterial>`	ExperimentalDesignUtils.`getOrderedSamples(ExpressionDataDoubleMatrix dmatrix, List<ExperimentalFactor> factors)`	This puts the control samples up front if possible.