Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips.
BACKGROUND
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.
Bjork
Kathe E
KE
Department of Mathematical Sciences, University of Colorado at Denver and Health Sciences Center, Denver, CO 80217, USA. Kathe.bjork@cudenver.edu
Kafadar
Karen
K
D016477:Artifacts; D004867:Equipment Design; D019544:Equipment Failure Analysis; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity