Paper Info
Title
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. Contact: Kathe.bjork@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/.
Year
DOI
Venue
2007
10.1093/bioinformatics/btm450
Bioinformatics
Field
DocType
Volume
Automatic summarization,Data mining,Differential expression,Normalization (statistics),Computer science,Profiling (computer programming),Bioinformatics,Cluster analysis
Journal
23
Issue
ISSN
Citations 
21
1367-4803
0
PageRank 
References 
Authors
0.34
3
2
Name
Order
Citations
PageRank
Kathe E. Bjork100.34
Karen Kafadar2466.32