Method
Towards the uniform distribution of null P values on Affymetrix microarrays
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
Genome Biology 2007, 8:R69 doi:10.1186/gb-2007-8-5-r69
Published: 1 May 2007Abstract
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.
