Affymetrix GeneChip microarray preprocessing for multivariate analyses.

ABSTRACT: 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

SUBMITTER: McCall MN 

PROVIDER: S-EPMC3431718 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature