Affymetrix GeneChip microarray preprocessing for multivariate analyses.
Affymetrix GeneChip microarrays are the most widely used high-throughput technology to measure gene expression, and a wide variety of preprocessing methods have been developed to transform probe intensities reported by a microarray scanner into gene expression estimates. There have been numerous comparisons of these preprocessing methods, focusing on the most common analyses-detection of differential expression and gene or sample clustering. Recently, more complex multivariate analyses, such as gene co-expression, differential co-expression, gene set analysis and network modeling, are becoming more common; however, the same preprocessing methods are typically applied. In this article, we examine the effect of preprocessing methods on some of these multivariate analyses and provide guidance to the user as to which methods are most appropriate.
Department of Biostatistics and Computational Biology, University of Rochester Medical Center, NY, USA. mccallm@gmail.com
Matthew N
MN
McCall
Anthony
A
Almudevar
D016000:Cluster Analysis; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D015999:Multivariate Analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*