AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs.

ABSTRACT:

Background

Affymetrix gene expression arrays incorporate paired perfect match (PM) and mismatch (MM) probes to distinguish true signals from those arising from cross-hybridization events. A MM signal often shows greater intensity than a PM signal; we propose that one underlying cause is the presence of allelic variants arising from single nucleotide polymorphisms (SNPs). To annotate and characterize SNP contributions to anomalous probe binding behavior we have developed a software tool called AffyMAPSDetector.

Results

AffyMAPSDetector can be used to describe any Affymetrix expression GeneChip with respect to SNPs. When AffyMAPSDetector was run on GeneChip HG-U95Av2 against dbSNP-build-123, we found 7286 probes (belonging to 2,582 probesets) containing SNPs, out of which 325

SUBMITTER: Kumari S 

PROVIDER: S-EPMC1959249 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature