Exon arrays provide accurate assessments of gene expression.docVIP

Open Access M d 2007KapuretVoal.lumeetho8, Issue 5, Article R82 Exon arrays provide accurate assessments of gene expression Karen Kapur*, Yi Xing*?, Zhengqing Ouyang? and Wing Hung Wong* Addresses: *Department of Statistics, Stanford University, Stanford, California, 94305, USA. ?Department of Internal Medicine, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, USA. ?Department of Biological Sciences, Stanford University, Stanford, California, 94305, USA. Correspondence: Wing Hung Wong. Email: whwong@ Published: 15 May 2007 Received: 11 December 2006 Revised: 2 April 2007 Accepted: 15 May 2007 Genome Biology 2007, 8:R82 (doi:10.1186/gb-2007-8-5-r82) The electronic version of this article is the complete one and can be found online at /2007/8/5/R82 ? 2007 Kapur 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. mGenepenAtsexpressionsotfragteengeyefoxpronreessexontsimioantarraysingthangenetradexpressionitional 3’ aronrayAffymetrixs./p exon arrays suggests that these arrays may provide more accurate measure- Abstract We have developed a strategy for estimating gene expression on Affymetrix Exon arrays. The method includes a probe-specific background correction and a probe selection strategy in which a subset of probes with highly correlated intensities across multiple samples are chosen to summarize gene expression. Our results demonstrate that the proposed background model offers improvements over the default Affymetrix background correction and that Exon arrays may provide more accurate measurements of gene expression than traditional 3 arrays. Background purely computational predictions (full probes). In contrast to the 3 approa