Package ubic.erminej.analysis

Interface Summary

Interface	Description
NullDistributionGenerator

Class Summary

Class	Description
AbstractGeneSetPvalGenerator	Base implementation of pvalue generator
AbstractLongTask
AbstractResamplingGeneSetScore
CorrelationPvalGenerator
ExperimentScoreQuickPvalGenerator	Does the same thing as GeneSetResamplingPvalGeneratorbut is stripped-down for using during resampling.
GeneSetPvalRun	Class that does all the work in doing gene set scoring.
GeneSetResamplingBackgroundDistributionGenerator	Calculates a background distribution for class scores derived from randomly selected individual gene scores.
GeneSetResamplingPvalGenerator	Generates gene set p values using the resampling-based 'experiment score' method of Pavlidis et al.
MultipleTestCorrector	Perform multiple test correction on class scores.
OraPvalGenerator	Compute gene set scores based on over-representation analysis (ORA).
ResamplingCorrelationGeneSetScore
RocPvalGenerator	Compute gene set p values based on the receiver operating characteristic (ROC).
ScoreQuantiles