Correcting for sequence biases in present/absent calls
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
Genome Biology 2007, 8:R125 doi:10.1186/gb-2007-8-6-r125Published: 26 June 2007
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.