Conservative adjustment of permutation p-values when the number of permutations is limited
by Yinglei Lai
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 3, No. 4, 2007

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.

Online publication date: Mon, 15-Oct-2007

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