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

Class AbstractDifferentialExpressionAnalyzer

java.lang.Object

ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer

ubic.gemma.core.analysis.expression.diff.AbstractDifferentialExpressionAnalyzer

All Implemented Interfaces:

DiffExAnalyzer

Direct Known Subclasses:

LinearModelAnalyzer

public abstract class AbstractDifferentialExpressionAnalyzer
extends AbstractAnalyzer
implements DiffExAnalyzer

An abstract differential expression analyzer to be extended

Author:

keshav

Field Summary

Fields inherited from class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer

compositeSequenceService, expressionDataMatrixService

Constructor Summary

Constructors

Constructor	Description
AbstractDifferentialExpressionAnalyzer()

Method Summary

Modifier and Type	Method	Description
abstract Collection<DifferentialExpressionAnalysis>	run(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
abstract Collection<DifferentialExpressionAnalysis>	run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Allows entry of modified data matrices into the workflow.

Methods inherited from class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer

setExpressionDataMatrixService

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer

computeHitListSizes, determineInterceptFactor, getNumberOfGenesTested, run, setExpressionDataMatrixService

Constructor Detail

AbstractDifferentialExpressionAnalyzer

public AbstractDifferentialExpressionAnalyzer()

Method Detail

run

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

Specified by:

run in interface DiffExAnalyzer

Parameters:

expressionExperiment - the experiment

config - config

Returns:

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

run

public abstract Collection<DifferentialExpressionAnalysis> run(ExpressionExperiment expressionExperiment,
                                                               ExpressionDataDoubleMatrix dmatrix,
                                                               DifferentialExpressionAnalysisConfig config)

Description copied from interface: DiffExAnalyzer

Allows entry of modified data matrices into the workflow.

Specified by:

run in interface DiffExAnalyzer

Parameters:

expressionExperiment - the experiment

dmatrix - D matrix

config - config

Returns:

analyses