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Open Access Method

Correcting for sequence biases in present/absent calls

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

Author Affiliations

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

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

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

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Genome Biology 2007, 8:R125  doi:10.1186/gb-2007-8-6-r125

Published: 26 June 2007

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.