Widespread existence of uncorrelated probe intensities from within the same probeset on Affymetrix GeneChips

Abstract

We have developed a computational pipeline to analyse large surveys of A ymetrix GeneChips, for example NCBI’s Gene Expression Omnibus. GEO samples data for many organisms, tissues and phenotypes. Because of this experimental diversity, any observed correlations between probe intensities can be associated either with biology that is robust, such as common co-expression, or with systematic biases associated with the GeneChip technology.