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

Interface DiffExAnalyzer

All Known Implementing Classes:

LinearModelAnalyzer

public interface DiffExAnalyzer

Author:

paul

Method Summary

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	run(ExpressionExperiment expressionExperiment, Map<FactorValue,ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset with a pre-existing subset structure.
Collection<DifferentialExpressionAnalysis>	run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset.
DifferentialExpressionAnalysis	run(ExpressionExperimentSubSet subset, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a subset.

Method Details

run

Collection<DifferentialExpressionAnalysis> run(ExpressionExperiment expressionExperiment,
 ExpressionDataDoubleMatrix dmatrix,
 DifferentialExpressionAnalysisConfig config)
                                        throws AnalysisException

Analyze a dataset.

Parameters:

expressionExperiment - experiment to analyze

dmatrix - D matrix

config - config

Returns:

analyses. There will be more than one if a subset factor is defined.

Throws:

AnalysisException

run

Collection<DifferentialExpressionAnalysis> run(ExpressionExperiment expressionExperiment,
 Map<FactorValue,ExpressionExperimentSubSet> subsets,
 ExpressionDataDoubleMatrix dmatrix,
 DifferentialExpressionAnalysisConfig config)
                                        throws AnalysisException

Analyze a dataset with a pre-existing subset structure.

A subset must be defined in the configuration.

Throws:

AnalysisException

run

DifferentialExpressionAnalysis run(ExpressionExperimentSubSet subset,
 ExpressionDataDoubleMatrix dmatrix,
 DifferentialExpressionAnalysisConfig config)
                            throws AnalysisException

Analyze a subset.

Note that normally when we run a subset analysis, the subsetting is done internally, so we pass in the expression experiment, not the subset. This method is used for exceptions to that.

Parameters:

subset - subset

config - config

Returns:

analysis

Throws:

AnalysisException