Package ubic.gemma.model.analysis.expression.diff

Class ExpressionAnalysisResultSet

java.lang.Object

ubic.gemma.model.analysis.AnalysisResultSet<R>

ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet<DifferentialExpressionAnalysisResult>

ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet

All Implemented Interfaces:

gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Serializable, Securable, SecuredChild, Identifiable

public class ExpressionAnalysisResultSet
extends FactorAssociatedAnalysisResultSet<DifferentialExpressionAnalysisResult>
implements SecuredChild

A group of results for an ExpressionExperiment.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ExpressionAnalysisResultSet.Factory

Constructor Summary

Constructors

Constructor	Description
ExpressionAnalysisResultSet()

Method Summary

Modifier and Type	Method	Description
DifferentialExpressionAnalysis	getAnalysis()
FactorValue	getBaselineGroup()
Set<HitListSize>	getHitListSizes()
Integer	getNumberOfGenesTested()
Integer	getNumberOfProbesTested()
PvalueDistribution	getPvalueDistribution()
Set<DifferentialExpressionAnalysisResult>	getResults()
Securable	getSecurityOwner()
void	setAnalysis(DifferentialExpressionAnalysis analysis)
void	setBaselineGroup(FactorValue baselineGroup)
void	setHitListSizes(Set<HitListSize> hitListSizes)
void	setNumberOfGenesTested(Integer numberOfGenesTested)
void	setNumberOfProbesTested(Integer numberOfProbesTested)
void	setPvalueDistribution(PvalueDistribution pvalueDistribution)
void	setResults(Set<DifferentialExpressionAnalysisResult> results)
String	toString()

Methods inherited from class ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet

getExperimentalFactors, setExperimentalFactors

Methods inherited from class ubic.gemma.model.analysis.AnalysisResultSet

equals, getId, hashCode, setId

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ubic.gemma.model.common.Identifiable

getId

Methods inherited from interface gemma.gsec.model.Securable

getId

Constructor Detail

ExpressionAnalysisResultSet

public ExpressionAnalysisResultSet()

Method Detail

toString

public String toString()

Overrides:

toString in class Object

getAnalysis

public DifferentialExpressionAnalysis getAnalysis()

setAnalysis

public void setAnalysis(DifferentialExpressionAnalysis analysis)

getBaselineGroup

@Nullable
public FactorValue getBaselineGroup()

Returns:

The group considered baseline when computing scores and 'upRegulated'. This might be a control group if it could be recognized. For continuous factors, this would be null. For interaction terms we do not compute this so it will also be null.

setBaselineGroup

public void setBaselineGroup(FactorValue baselineGroup)

getHitListSizes

public Set<HitListSize> getHitListSizes()

setHitListSizes

public void setHitListSizes(Set<HitListSize> hitListSizes)

getNumberOfGenesTested

public Integer getNumberOfGenesTested()

Returns:

How many genes were tested in the result set. This is determined based on the annotations at one point in time, so might slightly differ if the platform annotations have been updated since.

setNumberOfGenesTested

public void setNumberOfGenesTested(Integer numberOfGenesTested)

getNumberOfProbesTested

public Integer getNumberOfProbesTested()

Returns:

How many probes were tested in this result set.

setNumberOfProbesTested

public void setNumberOfProbesTested(Integer numberOfProbesTested)

getPvalueDistribution

public PvalueDistribution getPvalueDistribution()

setPvalueDistribution

public void setPvalueDistribution(PvalueDistribution pvalueDistribution)

getResults

public Set<DifferentialExpressionAnalysisResult> getResults()

setResults

public void setResults(Set<DifferentialExpressionAnalysisResult> results)

getSecurityOwner

public Securable getSecurityOwner()

Specified by:

getSecurityOwner in interface gemma.gsec.model.SecuredChild

Specified by:

getSecurityOwner in interface SecuredChild