Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity.

ABSTRACT:

Background

RNA and microarray quality assessment form an integral part of gene expression analysis and, although methods such as the RNA integrity number (RIN) algorithm reliably asses RNA integrity, the relevance of RNA integrity in gene expression analysis as well as analysis methods to accommodate the possible effects of degradation requires further investigation. We investigated the relationship between RNA integrity and array quality on the commonly used Affymetrix Gene 1.0 ST array platform using reliable within-array and between-array quality assessment measures. The possibility of a transcript specific bias in the apparent effect of RNA degradation on the measured gene expression signal was evaluated after either excluding quality-flagged arrays or compensation for RNA degr

SUBMITTER: Viljoen KS 

PROVIDER: S-EPMC3557148 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature