Correcting for sequence biases in present/absent calls

Eugene F Schuster¹ , Eric Blanc² , Linda Partridge³ and Janet M Thornton¹

¹European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK

²MRC Centre for Developmental Neurobiology, King's College London, Guy's Hospital Campus, London SE1 1UL, UK

³Department of Biology, University College London, Gower Street, London WC1E 6BT, UK

author email corresponding author email

Genome Biology 2007, 8:R125doi:10.1186/gb-2007-8-6-r125


Published:	26 June 2007

Subject areas: Bioinformatics, Genome studies

Abstract

The probe sequence of short oligonucleotides in Affymetrix microarray experiments can have a significant influence on present/absent calls of probesets with absent target transcripts. Probesets enriched for central Ts and depleted of central As in the perfect-match probes tend to be falsely classified as having present transcripts. Correction of non-specific binding for both perfect-match and mismatch probes using probe-sequence models can partially remove the probe-sequence bias and result in better performance of the MAS 5.0 algorithm.