biostudies-literatureSchuster EFMedical Research CouncilWellcome TrustBiotechnology and Biological Sciences Research CouncilR125https://www.ebi.ac.uk/biostudies/studies/S-EPMC2394774biostudies-literatureUnknown8(6)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.Genome biologyCorrecting for sequence biases in present/absent calls.PMC2394774G9900989SF19106Blanc ESchuster EFPartridge LThornton JMfalseCorrecting for sequence biases in present/absent calls.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.2007-01-01T00:00:00Z20072025-04-19T07:40:52.147Z2019-03-27T00:15:12ZS-EPMC23947741759449210.1186/gb-2007-8-6-r125