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

• Published in: Bioinformatics 2007-11, Vol.23 (21), p.2873-2880
• Main Authors: Bjork, Kathe E., Kafadar, Karen
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; Equipment Design; Equipment Failure Analysis; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - instrumentation; Gene Expression Profiling - methods; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Oligonucleotide Array Sequence Analysis - instrumentation; Oligonucleotide Array Sequence Analysis - methods; Reproducibility of Results; Sensitivity and Specificity
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btm450

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: [e-mail] 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/.