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

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. © The Author 2007. Published by Oxford University Press. All rights reserved.