baseCode.math
Class MultipleTestCorrection

java.lang.Object
  baseCode.math.MultipleTestCorrection

public class MultipleTestCorrection

extends java.lang.Object

Methods for p-value correction of sets of hypothesis tests.

Copyright (c) 2004

Institution:: Columbia University

Version:

$Id: MultipleTestCorrection.java,v 1.6 2004/07/27 03:18:57 pavlidis Exp $

Author:

Paul Pavlidis

Constructor Summary

MultipleTestCorrection()

Method Summary

static double	BenjaminiHochbergCut(cern.colt.list.DoubleArrayList pvalues, double fdr) Benjamini-Hochberg method.
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).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MultipleTestCorrection

public MultipleTestCorrection()

Method Detail

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

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

Returns:

The maximum pvalue that maintains the false discovery rate