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Bioinformatics. 2009 Jun 15;25(12):i161-8. doi: 10.1093/bioinformatics/btp211.

Fewer permutations, more accurate P-values.

Author information

1
Institute for Systems Biology, Seattle, WA, USA. tknijnenburg@systemsbiology.org

Abstract

MOTIVATION:

Permutation tests have become a standard tool to assess the statistical significance of an event under investigation. The statistical significance, as expressed in a P-value, is calculated as the fraction of permutation values that are at least as extreme as the original statistic, which was derived from non-permuted data. This empirical method directly couples both the minimal obtainable P-value and the resolution of the P-value to the number of permutations. Thereby, it imposes upon itself the need for a very large number of permutations when small P-values are to be accurately estimated. This is computationally expensive and often infeasible.

RESULTS:

A method of computing P-values based on tail approximation is presented. The tail of the distribution of permutation values is approximated by a generalized Pareto distribution. A good fit and thus accurate P-value estimates can be obtained with a drastically reduced number of permutations when compared with the standard empirical way of computing P-values.

AVAILABILITY:

The Matlab code can be obtained from the corresponding author on request.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
19477983
PMCID:
PMC2687965
DOI:
10.1093/bioinformatics/btp211
[Indexed for MEDLINE]
Free PMC Article

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