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Bioinformatics Advance Access published online on September 25, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm450
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Systematic order dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips®

Kathe E. Bjork 1,2,* and Karen Kafadar 1

1Department of Mathematical Sciences, University of Colorado at Denver and Health Sciences Center, Denver, CO 80217, 2PriMetrics, Inc., Arvada, CO 80007

*To whom correspondence should be addressed. Dr. Kathe E. Bjork, E-mail: kathe.bjork{at}cudenver.edu


  Abstract

Motivation: Affymetrix GeneChips® are common 3’ profiling platforms for quantifying gene expression. Using publicly available datasets of expression profiles from human and mouse experiments, we sought to characterize features of GeneChip® data to better compare and evaluate analyses for differential expression, regulation and clustering. We uncovered an unexpected order dependence in expression data that holds across a variety of chips in both human and mouse data.

Results: Order dependence among GeneChips® affected relative expression measures pre-processed and normalized with the Affymetrix MAS5.0 algorithm and the robust multi-array average summarization method. The effect strongly influenced detection calls and tests for differential expression and can potentially significantly bias experimental results based on GeneChip® profiling.

Contact: kathe.bjork{at}cudenver.edu

Associate Editor: Dr. Joaquin Dopazo

Received on June 17, 2007; revised on August 24, 2007; accepted on August 25, 2007

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