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

Packages that use ExpressionDataDoubleMatrix

Package	Description
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.
ubic.gemma.persistence.service.expression.bioAssayData

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

Classes in ubic.gemma.core.analysis.expression.diff that implement interfaces with type arguments of type ExpressionDataDoubleMatrix

Modifier and Type	Class	Description
class	DifferentialExpressionAnalysisFilter	Filter used for performing DEA.

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

Modifier and Type	Method	Description
static ExpressionDataDoubleMatrix	DiffExAnalyzerUtils.dropSamplesNotAnalyzed(ExpressionDataDoubleMatrix dmatrix)	Remove the samples that are not analyzed (see DiffExAnalyzerUtils.isAnalyzed(BioMaterial)) from a data matrix.
ExpressionDataDoubleMatrix	DifferentialExpressionAnalysisFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	DifferentialExpressionAnalysisFilter.filter(ExpressionDataDoubleMatrix dataMatrix, DifferentialExpressionAnalysisFilterResult filterResult)

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

Modifier and Type	Method	Description
static ExpressionDataDoubleMatrix	DiffExAnalyzerUtils.dropSamplesNotAnalyzed(ExpressionDataDoubleMatrix dmatrix)	Remove the samples that are not analyzed (see DiffExAnalyzerUtils.isAnalyzed(BioMaterial)) from a data matrix.
ExpressionDataDoubleMatrix	DifferentialExpressionAnalysisFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	DifferentialExpressionAnalysisFilter.filter(ExpressionDataDoubleMatrix dataMatrix, DifferentialExpressionAnalysisFilterResult filterResult)
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)	Check if a factor value should be excluded from the analysis.

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)

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)

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

Classes in ubic.gemma.core.analysis.preprocess.filter that implement interfaces with type arguments of type ExpressionDataDoubleMatrix

Modifier and Type	Class	Description
class	AffyProbeNameFilter
class	ExpressionExperimentFilter	Default filter used for various analyses of expression experiments.
class	LowVarianceFilter	Filter rows with low variance by keeping those with variance above a given cut-off.
class	MinimumCellsFilter	Filter that removes samples that do not meet a minimum number of cells requirement.
class	OutliersFilter	Filter that removes outliers from expression data by masking them with Double.NaN.
class	RepetitiveValuesFilter	Filter design elements with repetitive values across samples.
class	RowMissingValueFilter	Filter out rows that have "too many" missing values.
class	RowsWithSequencesFilter	Only retain design elements that have a BioSequence associated.
class	TooFewDistinctValuesFilter	Remove rows that have a low diversity of values (equality judged based on tolerance set in RowLevelFilter).
class	ZeroVarianceFilter	Remove rows that have a variance of zero (within a small constant)

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 dataMatrix, Collection<ArrayDesign> arrayDesignsUsed, ExpressionExperimentFilterResult result)
ExpressionDataDoubleMatrix	ExpressionExperimentFilter.filter(ExpressionDataDoubleMatrix dataMatrix, ExpressionExperimentFilterResult result)
ExpressionDataDoubleMatrix	LowVarianceFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	MinimumCellsFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	OutliersFilter.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
boolean	LowVarianceFilter.appliesTo(ExpressionDataDoubleMatrix dataMatrix)
boolean	MinimumCellsFilter.appliesTo(ExpressionDataDoubleMatrix dataMatrix)
boolean	RepetitiveValuesFilter.appliesTo(ExpressionDataDoubleMatrix dataMatrix)
boolean	TooFewDistinctValuesFilter.appliesTo(ExpressionDataDoubleMatrix dataMatrix)
static int	ExpressionDataFilterUtils.countSamplesWithData(ExpressionDataDoubleMatrix dataMatrix)	Count the number of samples in the given matrix.
ExpressionDataDoubleMatrix	AffyProbeNameFilter.filter(ExpressionDataDoubleMatrix data)
ExpressionDataDoubleMatrix	ExpressionExperimentFilter.filter(ExpressionDataDoubleMatrix matrix)
ExpressionDataDoubleMatrix	ExpressionExperimentFilter.filter(ExpressionDataDoubleMatrix dataMatrix, Collection<ArrayDesign> arrayDesignsUsed, ExpressionExperimentFilterResult result)
ExpressionDataDoubleMatrix	ExpressionExperimentFilter.filter(ExpressionDataDoubleMatrix dataMatrix, ExpressionExperimentFilterResult result)
ExpressionDataDoubleMatrix	LowVarianceFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	MinimumCellsFilter.filter(ExpressionDataDoubleMatrix dataMatrix)
ExpressionDataDoubleMatrix	OutliersFilter.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)
static Set<BioMaterial>	ExpressionDataFilterUtils.getSamplesWithData(ExpressionDataDoubleMatrix dataMatrix)	Obtain the set of samples (columns) with data.

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, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform, ExpressionExperimentFilterResult result)	Provide a filtered expression data matrix, reporting the per-stage attrition into a caller-supplied result.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, ExpressionExperimentFilterConfig filterConfig)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors, ArrayDesign arrayDesign, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform, ExpressionExperimentFilterResult result)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, ExpressionExperimentFilterConfig 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.sliceColumns(List<BioMaterial> bioMaterials)
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension reorderedDim)
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.withMatrix(DoubleMatrix<CompositeSequence, BioMaterial> matrix)	Create a copy of this matrix with the given data matrix.
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.withMatrix(DoubleMatrix<CompositeSequence, BioMaterial> matrix, Map<QuantitationType, QuantitationType> quantitationTypes)	Create a copy of this matrix with the given data matrix and quantitation types.
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.withNumberOfCells(int[][] numberOfCells)

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, int[][] numberOfCells)

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.persistence.service.expression.bioAssayData

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

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	ProcessedExpressionDataVectorService.computeUnmaskedProcessedDataMatrix(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)	Rebuild the processed data matrix from raw WITHOUT masking assays flagged as outliers, persisting nothing.
ExpressionDataDoubleMatrix	ProcessedExpressionDataVectorServiceImpl.computeUnmaskedProcessedDataMatrix(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)