ubic.erminej.analysis

Class MultipleTestCorrector

java.lang.Object

ubic.erminej.analysis.AbstractLongTask

ubic.erminej.analysis.MultipleTestCorrector

public class MultipleTestCorrector
extends AbstractLongTask

Perform multiple test correction on class scores. Multiple test correction is based on the non-redundant set of gene sets, to avoid overcorrecting.

Version:

$Id: MultipleTestCorrector.java,v 1.20 2013/04/07 04:33:14 paul Exp $

Author:

Paul Pavlidis

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Constructor and Description
MultipleTestCorrector(SettingsHolder set, List<GeneSetTerm> sc, GeneAnnotations geneData, GeneScores geneScores, Map<GeneSetTerm,GeneSetResult> results, StatusViewer messenger)

Method Summary

Methods

Modifier and Type	Method and Description
void	benjaminihochberg() Benjamini-Hochberg correction of pvalues.
void	bonferroni() Bonferroni correction of class pvalues.
void	westfallyoung() Run WY with a default number of trials.
void	westfallyoung(int trials) Westfall-Young pvalue correction.

Methods inherited from class ubic.erminej.analysis.AbstractLongTask

ifInterruptedStop

Methods inherited from class java.lang.Object

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

Field Detail

log

protected static final org.apache.commons.logging.Log log

Constructor Detail

MultipleTestCorrector

public MultipleTestCorrector(SettingsHolder set,
                     List<GeneSetTerm> sc,
                     GeneAnnotations geneData,
                     GeneScores geneScores,
                     Map<GeneSetTerm,GeneSetResult> results,
                     StatusViewer messenger)

Parameters:

set -

sc -

geneData -

geneScores - - only used for Westfall-Young

results -

messenger -

Method Detail

benjaminihochberg

public void benjaminihochberg()

Benjamini-Hochberg correction of pvalues. Default method, used for GUI

Parameters:

fdr - double desired false discovery rate.

bonferroni

public void bonferroni()

Bonferroni correction of class pvalues.

westfallyoung

public void westfallyoung()

Run WY with a default number of trials.

See Also:

westfallyoung(numtrials)

westfallyoung

public void westfallyoung(int trials)

Westfall-Young pvalue correction. Based on algorithm 2.8, pg 66 of 'Resampling-based Multiple Testing'.

1. Sort the pvalues for the real data (assume worst pvalue is first)
2. Make an array of count variables, one for each class, intialize to zero. loop: (n=10,000).
3. Generate class pvalues for randomized values (see above); 3. Iterate over this in the same order as the actual order.
4. Define successive minima: (q is the trial; p is real, already ranked)
   1. a. qk = pk (class with worst pvalue)
   2. b. qk-1 = min (qk, pk-1) ...
5. at each step a.... if qi <= pi, count_i++ end loop.
6. p_i* = count_i/n 7. enforce monotonicity by using successive maximization.

Parameters:

trials - How many random trials to do. According to W-Y, it should be >=10,000.