European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. schuster@ebi.ac.uk
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.