Towards the uniform distribution of null P values on Affymetrix microarrays.
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.
Fodor
Anthony A
AA
Bioinformatics Resource Center, The University of North Carolina at Charlotte, University City Boulevard, Charlotte, North Carolina 28223, USA. anthony.fodor@gmail.com
Tickle
Timothy L
TL
Richardson
Christine
C
D003429:Cross Reactions; D005189:False Positive Reactions; D046228:Microarray Analysis / Q000592:standards / Q000706:statistics & numerical data*; D015233:Models, Statistical; D009693:Nucleic Acid Hybridization