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Open Access Method

Towards the uniform distribution of null P values on Affymetrix microarrays

Anthony A Fodor1*, Timothy L Tickle1 and Christine Richardson12

Author Affiliations

1 Bioinformatics Resource Center, The University of North Carolina at Charlotte, University City Boulevard, Charlotte, North Carolina 28223, USA

2 Department of Biology, The University of North Carolina at Charlotte, University City Boulevard, Charlotte, North Carolina 28223, USA

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Genome Biology 2007, 8:R69  doi:10.1186/gb-2007-8-5-r69

Published: 1 May 2007

Abstract

Methods to control false-positive rates require that P values of genes that are not differentially expressed follow a uniform distribution. Commonly used microarray statistics can generate P values that do not meet this assumption. We show that poorly characterized variance, imperfect normalization, and cross-hybridization are among the many causes of this non-uniform distribution. We demonstrate a simple technique that produces P values that are close to uniform for nondifferentially expressed genes in control datasets.