Correcting for sequence biases in present-absent callsReport as inadecuate

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Genome Biology

, 8:R125

First Online: 26 June 2007Received: 13 December 2006Revised: 11 May 2007Accepted: 26 June 2007


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.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2007-8-6-r125 contains supplementary material, which is available to authorized users.

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Author: Eugene F Schuster - Eric Blanc - Linda Partridge - Janet M Thornton


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