Title: Conservative adjustment of permutation p-values when the number of permutations is limited

Authors: Yinglei Lai

Addresses: Department of Statistics and Biostatistics Center, The George Washington University, 2140 Pennsylvania Avenue, NW, Washington DC 20052, USA

Abstract: In this study, we show through the theory of order statistics that a considerable proportion of p-values will be under-evaluated by the permutation procedure. To solve this problem, we propose to conservatively adjust permutation p-values. The adjustment requires no parametric assumption on the distribution of test statistics. The solution can be expressed by a normalised incomplete beta function. The related normal distribution approximation is also discussed. Simulations are conducted to illustrate the proposed method and two microarray gene expression data sets are considered for applications.

Keywords: p-values; limited permutation; microarrays; bioinformatics; order statistics; gene expression data.

DOI: 10.1504/IJBRA.2007.015420

International Journal of Bioinformatics Research and Applications, 2007 Vol.3 No.4, pp.536 - 546

Published online: 15 Oct 2007 *

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