Method

Exon arrays provide accurate assessments of gene expression

Karen Kapur¹ , Yi Xing^1,2 , Zhengqing Ouyang³ and Wing Hung Wong¹

¹Department of Statistics, Stanford University, Stanford, California, 94305, USA

²Department of Internal Medicine, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, USA

³Department of Biological Sciences, Stanford University, Stanford, California, 94305, USA

author email corresponding author email

Genome Biology 2007, 8:R82doi:10.1186/gb-2007-8-5-r82

Published:	15 May 2007

Subject areas: Bioinformatics, Genome studies

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.