Error control variability in pathway-based microarray analysis.

ABSTRACT:

Motivation

The decision to commit some or many false positives in practice rests with the investigator. Unfortunately, not all error control procedures perform the same. Our problem is to choose an error control procedure to determine a P-value threshold for identifying differentially expressed pathways in high-throughput gene expression studies. Pathway analysis involves fewer tests than differential gene expression analysis, on the order of a few hundred. We discuss and compare methods for error control for pathway analysis with gene expression data.

Results

In consideration of the variability in test results, we find that the widely used Benjamini and Hochberg's (BH) false discovery rate (FDR) analysis is less robust than alternative procedures. BH's error control require

SUBMITTER: Gold DL 

PROVIDER: S-EPMC2734315 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature