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

Class AnalysisSelectionAndExecutionServiceImpl

java.lang.Object

ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl

All Implemented Interfaces:

Aware, ApplicationContextAware, AnalysisSelectionAndExecutionService

@Component
public class AnalysisSelectionAndExecutionServiceImpl
extends Object
implements AnalysisSelectionAndExecutionService

A differential expression analysis tool that executes the appropriate analysis based on the number of experimental factors and factor values, as well as the block design. Implementations of the selected analyses; t-test, one way anova, and two way anova with and without interactions are based on the details of the paper written by P. Pavlidis, Methods 31 (2003) 282-289. See http://www.bioinformatics.ubc.ca/pavlidis/lab/docs/reprints/anova-methods.pdf.

Author:

keshav

Constructor Summary

Constructors

Constructor	Description
AnalysisSelectionAndExecutionServiceImpl()

Method Summary

Modifier and Type	Method	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 includeInteractionsIfPossible)	FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
DifferentialExpressionAnalyzerServiceImpl.AnalysisType	determineAnalysis(BioAssaySet bioAssaySet, DifferentialExpressionAnalysisConfig config)	FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
DiffExAnalyzer	getAnalyzer()
void	setApplicationContext(ApplicationContext applicationContext)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AnalysisSelectionAndExecutionServiceImpl

public AnalysisSelectionAndExecutionServiceImpl()

Method Detail

analyze

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

Specified by:

analyze in interface AnalysisSelectionAndExecutionService

determineAnalysis

public DifferentialExpressionAnalyzerServiceImpl.AnalysisType determineAnalysis(BioAssaySet bioAssaySet,
                                                                                DifferentialExpressionAnalysisConfig config)

FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES

Specified by:

determineAnalysis in interface AnalysisSelectionAndExecutionService

Returns:

selected type of analysis such as t-test, two-way ANOVA, etc.

determineAnalysis

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

FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES

Specified by:

determineAnalysis in interface AnalysisSelectionAndExecutionService

Parameters:

bioAssaySet - bio assay set

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

subsetFactor - can be null

includeInteractionsIfPossible - if possible

Returns:

AnalysisType

getAnalyzer

public DiffExAnalyzer getAnalyzer()

Specified by:

getAnalyzer in interface AnalysisSelectionAndExecutionService

Returns:

a new instance of a linear model analyzer.

analyze

public DifferentialExpressionAnalysis analyze(ExpressionExperimentSubSet subset,
                                              DifferentialExpressionAnalysisConfig config)

Specified by:

analyze in interface AnalysisSelectionAndExecutionService

setApplicationContext

public void setApplicationContext(ApplicationContext applicationContext)
                           throws BeansException

Specified by:

setApplicationContext in interface ApplicationContextAware

Throws:

BeansException