Exon arrays provide accurate assessments of gene expression
1 Department of Statistics, Stanford University, Stanford, California, 94305, USA
2 Department of Internal Medicine, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, USA
3 Department of Biological Sciences, Stanford University, Stanford, California, 94305, USA
Genome Biology 2007, 8:R82 doi:10.1186/gb-2007-8-5-r82Published: 15 May 2007
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.