Interface GeneDifferentialExpressionService

    • 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

      • getDifferentialExpression

        Collection<DifferentialExpressionValueObject> getDifferentialExpression​(Gene gene,
                                                                                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