ubic.gemma.core.analysis.expression.diff

Interface AnalysisSelectionAndExecutionService

All Superinterfaces:

ApplicationContextAware, Aware

All Known Implementing Classes:

AnalysisSelectionAndExecutionServiceImpl

public interface AnalysisSelectionAndExecutionService
extends ApplicationContextAware

Author:

paul

Method Summary

Modifier and Type	Method and Description
Collection<DifferentialExpressionAnalysis>	analyze(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
DifferentialExpressionAnalysis	analyze(ExpressionExperimentSubSet subset, DifferentialExpressionAnalysisConfig config)
DifferentialExpressionAnalyzerServiceImpl.AnalysisType	determineAnalysis(BioAssaySet bioAssaySet, Collection<ExperimentalFactor> experimentalFactors, ExperimentalFactor subsetFactor, boolean includeInteractions) Determines the analysis to execute based on the experimental factors, factor values, and block design.
DifferentialExpressionAnalyzerServiceImpl.AnalysisType	determineAnalysis(BioAssaySet bioAssaySet, DifferentialExpressionAnalysisConfig config)
DiffExAnalyzer	getAnalyzer()

Methods inherited from interface org.springframework.context.ApplicationContextAware

setApplicationContext

Method Detail

analyze

Collection<DifferentialExpressionAnalysis> analyze(ExpressionExperiment expressionExperiment,
                                                   DifferentialExpressionAnalysisConfig config)

determineAnalysis

DifferentialExpressionAnalyzerServiceImpl.AnalysisType determineAnalysis(BioAssaySet bioAssaySet,
                                                                         DifferentialExpressionAnalysisConfig config)

determineAnalysis

DifferentialExpressionAnalyzerServiceImpl.AnalysisType determineAnalysis(BioAssaySet bioAssaySet,
                                                                         Collection<ExperimentalFactor> experimentalFactors,
                                                                         ExperimentalFactor subsetFactor,
                                                                         boolean includeInteractions)

Determines the analysis to execute based on the experimental factors, factor values, and block design.

Parameters:

experimentalFactors - which factors to use, or null if to use all from the experiment

subsetFactor - can be null

includeInteractions - if possible

bioAssaySet - bio assay set

Returns:

an appropriate analyzer

getAnalyzer

DiffExAnalyzer getAnalyzer()

Returns:

a new instance of a linear model analyzer.

analyze

DifferentialExpressionAnalysis analyze(ExpressionExperimentSubSet subset,
                                       DifferentialExpressionAnalysisConfig config)