Genome Biology
Volume 8
Issue 5 |
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 MethodTowards the uniform distribution of null P values on Affymetrix microarraysAnthony A Fodor1  , Timothy L Tickle1  and Christine Richardson1,2 1Bioinformatics Resource Center, The University of North Carolina at Charlotte, University City Boulevard, Charlotte, North Carolina 28223, USA 2Department of Biology, The University of North Carolina at Charlotte, University City Boulevard, Charlotte, North Carolina 28223, USA  author email corresponding author email
Genome Biology 2007,
8:R69doi:10.1186/gb-2007-8-5-r69
Subject areas: Bioinformatics, Genome studies, Immunology 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. | 
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