ubic.gemma.core.analysis.expression.diff

Interface GeneDifferentialExpressionService

All Known Implementing Classes:

GeneDifferentialExpressionServiceImpl

public interface GeneDifferentialExpressionService

Author:

paul

Field Summary

Fields

Modifier and Type	Field and Description
static double	PVALUE_CLIP_THRESHOLD p values smaller than this will be treated as this value in a meta-analysis.

Method Summary

Modifier and Type	Method and Description
ExperimentalFactorValueObject	configExperimentalFactorValueObject(ExperimentalFactor ef)
ExpressionExperimentValueObject	configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)
Collection<DifferentialExpressionValueObject>	getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees) Get the differential expression results for the given gene that is in a specified set of experiments.
Collection<DifferentialExpressionValueObject>	getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees, double threshold, int limit) Get the differential expression results for the given gene that is in a specified set of experiments.
Collection<DifferentialExpressionValueObject>	getDifferentialExpression(Gene gene, double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap) Get differential expression for a gene, constrained to a specific set of factors.
Collection<DifferentialExpressionValueObject>	getDifferentialExpression(Gene gene, double threshold, int limit) Get the differential expression results for the given gene across all datasets.
DifferentialExpressionMetaAnalysisValueObject	getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments) Get the differential expression analysis results for the gene in the activeExperiments.

Field Detail

PVALUE_CLIP_THRESHOLD

static final double PVALUE_CLIP_THRESHOLD

p values smaller than this will be treated as this value in a meta-analysis. The reason is to avoid extremely low pvalues from driving meta-pvalues down too fast. This is suggested by the fact that very small pvalues presume an extremely high precision in agreement between the tails of the true null distribution and the analytic distribution used to compute the pvalues (e.g., F or t).

See Also:

Constant Field Values

Method Detail

configExperimentalFactorValueObject

ExperimentalFactorValueObject configExperimentalFactorValueObject(ExperimentalFactor ef)

configExpressionExperimentValueObject

ExpressionExperimentValueObject configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)

getDifferentialExpression

Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
                                                                        Collection<BioAssaySet> ees)

Get the differential expression results for the given gene that is in a specified set of experiments.

Parameters:

gene - : gene of interest

ees - : set of experiments to search

Returns:

DEA VOs

getDifferentialExpression

Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
                                                                        Collection<BioAssaySet> ees,
                                                                        double threshold,
                                                                        int limit)

Get the differential expression results for the given gene that is in a specified set of experiments.

Parameters:

gene - : gene of interest

ees - : set of experiments to search

threshold - : the cutoff to determine if diff expressed

limit - : the maximum number of results to return (null for all)

Returns:

DEA VOs

getDifferentialExpression

Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
                                                                        double threshold,
                                                                        Collection<DiffExpressionSelectedFactorCommand> factorMap)

Get differential expression for a gene, constrained to a specific set of factors. Note that interactions are ignored, only main effects (the factorMap can only have one factor per experiment)

Parameters:

gene - gene

threshold - threshold

factorMap - factor map

Returns:

DEA VOs

getDifferentialExpression

Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
                                                                        double threshold,
                                                                        int limit)

Get the differential expression results for the given gene across all datasets.

Parameters:

threshold - threshold

gene - gene

limit - limit

Returns:

DEA VOs

getDifferentialExpressionMetaAnalysis

DifferentialExpressionMetaAnalysisValueObject getDifferentialExpressionMetaAnalysis(double threshold,
                                                                                    Gene g,
                                                                                    Map<Long,Long> eeFactorsMap,
                                                                                    Collection<BioAssaySet> activeExperiments)

Get the differential expression analysis results for the gene in the activeExperiments.

Parameters:

activeExperiments - active ees

eeFactorsMap - factor map

g - gene

threshold - threshold

Returns:

diff exp. analysis meta VO