Direct integration of intensity-level data from Affymetrix and Illumina microarrays improves statistical power for robust reanalysis.

ABSTRACT:

Background

Affymetrix GeneChips and Illumina BeadArrays are the most widely used commercial single channel gene expression microarrays. Public data repositories are an extremely valuable resource, providing array-derived gene expression measurements from many thousands of experiments. Unfortunately many of these studies are underpowered and it is desirable to improve power by combining data from more than one study; we sought to determine whether platform-specific bias precludes direct integration of probe intensity signals for combined reanalysis.

Results

Using Affymetrix and Illumina data from the microarray quality control project, from our own clinical samples, and from additional publicly available datasets we evaluated several approaches to directly integrate intensity

SUBMITTER: Turnbull AK 

PROVIDER: S-EPMC3443058 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature