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Genome Biol. 2007;8(6):R125.

Correcting for sequence biases in present/absent calls.

Author information

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

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.

PMID:
17594492
[PubMed - indexed for MEDLINE]
PMCID:
PMC2394774
Free PMC Article

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