Uses of Class
ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig

Packages that use DifferentialExpressionAnalysisConfig

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.service

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

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

Modifier and Type	Method	Description
static AnalysisType	DiffExAnalyzerUtils.determineAnalysisType(BioAssaySet bioAssaySet, DifferentialExpressionAnalysisConfig config)	FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
Collection<ExpressionAnalysisResultSet>	DifferentialExpressionAnalyzerService.extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate, DifferentialExpressionAnalysisConfig config)	Like redo, but we don't save the results, we just add the full set of results to the analysis given.
Collection<ExpressionAnalysisResultSet>	DifferentialExpressionAnalyzerServiceImpl.extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate, DifferentialExpressionAnalysisConfig baseConfig)
DifferentialExpressionAnalysis	DifferentialExpressionAnalyzerService.persistAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)	Made public for testing purposes only.
DifferentialExpressionAnalysis	DifferentialExpressionAnalyzerServiceImpl.persistAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)	Made public for testing purposes only.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> deas, DifferentialExpressionAnalysisConfig config, boolean ignoreFailingAnalyses)	Redo multiple analyses.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> deas, DifferentialExpressionAnalysisConfig config, boolean ignoreFailingAnalyses)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea, DifferentialExpressionAnalysisConfig config)	Redo an analysis.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea, DifferentialExpressionAnalysisConfig config)
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)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalyzerServiceImpl.runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
static void	DiffExAnalyzerUtils.writeConfig(DifferentialExpressionAnalysisConfig config, Writer writer)

Constructors in ubic.gemma.core.analysis.expression.diff with parameters of type DifferentialExpressionAnalysisConfig

Modifier	Constructor	Description
	AllAnalysesFailedException(String message, Collection<? extends AnalysisException> analysisExceptions, DifferentialExpressionAnalysisConfig config)
	AllSubSetAnalysesFailedException(String message, Collection<? extends AnalysisException> subsetExceptions, DifferentialExpressionAnalysisConfig config)
	AnalysisException(String message, DifferentialExpressionAnalysisConfig config)
	AnalysisException(Throwable cause, DifferentialExpressionAnalysisConfig config)
	DifferentialExpressionAnalysisConfig(DifferentialExpressionAnalysisConfig baseConfig)	Copy constructor.
	EbayesFailureException(Throwable cause, DifferentialExpressionAnalysisConfig config)
	InvalidQuantitationTypeConversionException(QuantitationTypeConversionException e, DifferentialExpressionAnalysisConfig config)
	NoFactorLeftForAnalysisException(String message, DifferentialExpressionAnalysisConfig config)
	NoSampleLeftForAnalysisException(String message, DifferentialExpressionAnalysisConfig config)

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

Methods in ubic.gemma.core.analysis.service with parameters of type DifferentialExpressionAnalysisConfig

Modifier and Type	Method	Description
void	DiffExAnalysisResultSetWriter.write(DifferentialExpressionAnalysis analysis, Map<CompositeSequence,String[]> geneAnnotations, DifferentialExpressionAnalysisConfig config, boolean hasSignificantBatchConfound, OutputStream stream)	Write a DifferentialExpressionAnalysis as a ZIP archive containing entries for the analysis and each result set.