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.

SUBMITTER: Schuster EF 

PROVIDER: S-EPMC2394774 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature