title: Correcting for sequence biases in present/absent calls.
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.
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. schuster@ebi.ac.uk
authors.forename: Eugene F
authors.initials: EF
authors.lastname: Schuster
authors.forename: Eric
authors.initials: E
authors.lastname: Blanc
authors.forename: Linda
authors.initials: L
authors.lastname: Partridge
authors.forename: Janet M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D000465:Algorithms; D000818:Animals; D020137:Base Pair Mismatch; D020029:Base Pairing; D004331:Drosophila melanogaster; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics*; D012313:RNA / Q000235:genetics
chemical_list: D015345:Oligonucleotide Probes; D012313:RNA