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Bioinformatics Advance Access originally published online on September 25, 2007
Bioinformatics 2007 23(21):2873-2880; 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 and 2PriMetrics Inc., Arvada, CO 80007, USA

*To whom correspondence should be addressed.


  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

Supplementary information: Supplementary Material, including links to files of ordered transcripts and supporting analyses, is available at the authors' websites, at http://www-math.cudenver.edu/~kbjork/research/, and http://www-math.cudenver.edu/~kk/research/.

Associate Editor: Joaquin Dopazo

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

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