Towards the uniform distribution of null P values on Affymetrix microarrays.

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.

SUBMITTER: Fodor AA 

PROVIDER: S-EPMC1929139 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature