Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity.

ABSTRACT:

Background

To identify differentially expressed genes (DEGs) from microarray data, users of the Affymetrix GeneChip system need to select both a preprocessing algorithm to obtain expression-level measurements and a way of ranking genes to obtain the most plausible candidates. We recently recommended suitable combinations of a preprocessing algorithm and gene ranking method that can be used to identify DEGs with a higher level of sensitivity and specificity. However, in addition to these recommendations, researchers also want to know which combinations enhance reproducibility.

Results

We compared eight conventional methods for ranking genes: weighted average difference (WAD), average difference (AD), fold change (FC), rank products (RP), moderated t statistic (modT), signific

SUBMITTER: Kadota K 

PROVIDER: S-EPMC2679019 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature