title: 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.
authors.affiliation: Bioinformatics Resource Center, The University of North Carolina at Charlotte, University City Boulevard, Charlotte, North Carolina 28223, USA. anthony.fodor@gmail.com
authors.forename: Anthony A
authors.initials: AA
authors.lastname: Fodor
authors.forename: Timothy L
authors.initials: TL
authors.lastname: Tickle
authors.forename: Christine
authors.initials: C
authors.lastname: Richardson
mesh_terms: D003429:Cross Reactions; D005189:False Positive Reactions; D046228:Microarray Analysis / Q000592:standards / Q000706:statistics & numerical data*; D015233:Models, Statistical; D009693:Nucleic Acid Hybridization