Collection<DifferentialExpressionAnalysis> |
AnalysisSelectionAndExecutionService.analyze(ExpressionExperiment expressionExperiment,
DifferentialExpressionAnalysisConfig config) |
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DifferentialExpressionAnalysis |
AnalysisSelectionAndExecutionService.analyze(ExpressionExperimentSubSet subset,
DifferentialExpressionAnalysisConfig config) |
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Collection<DifferentialExpressionAnalysis> |
AnalysisSelectionAndExecutionServiceImpl.analyze(ExpressionExperiment expressionExperiment,
DifferentialExpressionAnalysisConfig config) |
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DifferentialExpressionAnalysis |
AnalysisSelectionAndExecutionServiceImpl.analyze(ExpressionExperimentSubSet subset,
DifferentialExpressionAnalysisConfig config) |
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DifferentialExpressionAnalyzerServiceImpl.AnalysisType |
AnalysisSelectionAndExecutionService.determineAnalysis(BioAssaySet bioAssaySet,
DifferentialExpressionAnalysisConfig config) |
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DifferentialExpressionAnalyzerServiceImpl.AnalysisType |
AnalysisSelectionAndExecutionServiceImpl.determineAnalysis(BioAssaySet bioAssaySet,
DifferentialExpressionAnalysisConfig config) |
FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer 's
EXCLUDE_CHARACTERISTICS_VALUES
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DifferentialExpressionAnalysis |
DifferentialExpressionAnalyzerService.persistAnalysis(ExpressionExperiment expressionExperiment,
DifferentialExpressionAnalysis analysis,
DifferentialExpressionAnalysisConfig config) |
Made public for testing purposes only.
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DifferentialExpressionAnalysis |
DifferentialExpressionAnalyzerServiceImpl.persistAnalysis(ExpressionExperiment expressionExperiment,
DifferentialExpressionAnalysis analysis,
DifferentialExpressionAnalysisConfig config) |
Made public for testing purposes only.
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abstract Collection<DifferentialExpressionAnalysis> |
AbstractDifferentialExpressionAnalyzer.run(ExpressionExperiment expressionExperiment,
DifferentialExpressionAnalysisConfig config) |
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abstract Collection<DifferentialExpressionAnalysis> |
AbstractDifferentialExpressionAnalyzer.run(ExpressionExperiment expressionExperiment,
ExpressionDataDoubleMatrix dmatrix,
DifferentialExpressionAnalysisConfig config) |
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Collection<DifferentialExpressionAnalysis> |
DiffExAnalyzer.run(ExpressionExperiment expressionExperiment,
DifferentialExpressionAnalysisConfig config) |
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Collection<DifferentialExpressionAnalysis> |
DiffExAnalyzer.run(ExpressionExperiment expressionExperiment,
ExpressionDataDoubleMatrix dmatrix,
DifferentialExpressionAnalysisConfig config) |
Allows entry of modified data matrices into the workflow.
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DifferentialExpressionAnalysis |
DiffExAnalyzer.run(ExpressionExperimentSubSet subset,
DifferentialExpressionAnalysisConfig config) |
Note that normally when we run a subset analysis, the subsetting is done internally, so we pass in the expression
experiment, not the subset.
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Collection<DifferentialExpressionAnalysis> |
LinearModelAnalyzer.run(ExpressionExperiment expressionExperiment,
DifferentialExpressionAnalysisConfig config) |
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Collection<DifferentialExpressionAnalysis> |
LinearModelAnalyzer.run(ExpressionExperiment expressionExperiment,
ExpressionDataDoubleMatrix dmatrix,
DifferentialExpressionAnalysisConfig config) |
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DifferentialExpressionAnalysis |
LinearModelAnalyzer.run(ExpressionExperimentSubSet subset,
DifferentialExpressionAnalysisConfig config) |
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Collection<DifferentialExpressionAnalysis> |
DifferentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment,
DifferentialExpressionAnalysisConfig config) |
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Collection<DifferentialExpressionAnalysis> |
DifferentialExpressionAnalyzerServiceImpl.runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment,
DifferentialExpressionAnalysisConfig config) |
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