Towards the uniform distribution of null P values on Affymetrix microarrays 英文参考文献.docVIP

Open Access M d 2007FodoretVoal.lumeetho8, Issue 5, Article R69 Towards the uniform distribution of null P values on Affymetrix microarrays Anthony A Fodor*, Timothy L Tickle* and Christine Richardson*? Addresses: *Bioinformatics Resource Center, The University of North Carolina at Charlotte, University City Boulevard, Charlotte, North Carolina 28223, USA. ?Department of Biology, The University of North Carolina at Charlotte, University City Boulevard, Charlotte, North Carolina 28223, USA. Correspondence: Anthony A Fodor. Email: anthony.fodor@ Published: 1 May 2007 Received: 11 September 2006 Revised: 8 February 2007 Accepted: 1 May 2007 Genome Biology 2007, 8:R69 (doi:10.1186/gb-2007-8-5-r69) The electronic version of this article is the complete one and can be found online at /2007/8/5/R69 ? 2007 Fodor et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. UniformclposeErsttoimadistributionautninifgotrhme distoftrPimicroarraybu/tiitnv.al/upePfrvaluesom the overall distribution of scores on the microarray can produce itP /itvalues that are much 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. Background edges that biologists are often able to tolerate some error in gene lists. For example, a FDR could be