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 Schuster et al.; licensee BioMed Central Ltd.
Schuster, E. F., Blanc, E., Partridge, L., & Thornton, J. M. (2007). Correcting for sequence biases in present/absent calls. Genome Biology, 8(6). https://doi.org/10.1186/gb-2007-8-6-r125