Correcting positional correlations in Affymetrix® genome chips.

ABSTRACT: We report and model a previously undescribed systematic error causing spurious excess correlations that depend on the distance between probes on Affymetrix® microarrays. The phenomenon affects pairs of features with large chip separations, up to over 100 probes apart. The effect may have a significant impact on analysis of correlations in large collections of expression data, where the systematic experimental errors are repeated in many data sets. Examples of such studies include analysis of functions and interactions in groups of genes, as well as global properties of genomes. We find that the average correlations between probes on Affymetrix microarrays are larger for smaller chip distances, which points out to a previously undescribed positional artifact. The magnitude of the artifact d

SUBMITTER: Homouz D 

PROVIDER: S-EPMC4649851 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature