Package ubic.basecode.math

Class MultipleTestCorrection

  • public class MultipleTestCorrection
extends Object
    Methods for p-value correction of sets of hypothesis tests.

    FIXME make this API more consistent.

    Author:
    Paul Pavlidis

    • Constructor Detail

      • MultipleTestCorrection

        public MultipleTestCorrection()

    • Method Detail

      • benjaminiHochberg

        public static cern.colt.list.DoubleArrayList benjaminiHochberg​(cern.colt.list.DoubleArrayList pvalues)
        Parameters:
        pvalues -
        Returns:
        false discovery rates (FDR) computed using the method of Benjamini and Hochberg. The order is the same as the original pvalues (that is, each value fdr[i] corresponds to the pvaluesp[i].

      • benjaminiHochberg

        public static cern.colt.matrix.DoubleMatrix1D benjaminiHochberg​(cern.colt.matrix.DoubleMatrix1D pvalues)
        Parameters:
        pvalues - ; can contain missing values or invalid pvalues (outside range [0-1]), which are ignored.
        Returns:
        false discovery rates (FDRs) computed using the method of Benjamini and Hochberg; or null if they could not be computed. The order is the same as the original pvalues (that is, each value fdr[i] corresponds to the pvaluesp[i].

      • benjaminiHochbergCut

        public static double benjaminiHochbergCut​(cern.colt.list.DoubleArrayList pvalues,
                                          double fdr)
        Benjamini-Hochberg method. Determines the maximum p value to maintain the false discovery rate. (Assuming pvalues are independent);
        Parameters:
        pvalues - list of pvalues. Need not be sorted.
        fdr - false discovery rate (value q in B-H).
        Returns:
        The maximum pvalue that maintains the false discovery rate
        Throws:
        IllegalArgumentException - if invalid pvalues are encountered.

      • BenjaminiYekuteliCut

        public static double BenjaminiYekuteliCut​(cern.colt.list.DoubleArrayList pvalues,
                                          double fdr)
        Benjamini-Yekuteli method. Determines the maximum p value to maintain the false discovery rate. Valid under dependence of the pvalues. This method is more conservative than Benjamini-Hochberg.
        Parameters:
        pvalues - list of pvalues. Need not be sorted.
        fdr - false discovery rate (value q in B-H).
        Returns:
        The maximum pvalue that maintains the false discovery rate
        Throws:
        IllegalArgumentException - if invalid pvalues are encountered.

      • BonferroniCut

        public static double BonferroniCut​(cern.colt.list.DoubleArrayList pvalues,
                                   double fwe)
        Determine the Bonferroni pvalue threshold to maintain the family wise error rate (assuming pvalues are independent).
        Parameters:
        pvalues - The pvalues
        fwe - The family wise error rate
        Returns:
        The minimum pvalue that maintains the FWE