Motivation: We consider the problem of estimating values associated with gene expression from oligonucleotide arrays. Such estimates should linearly track concentration, yield non-negative results, have statistical guarantees of robustness against outliers, and allow estimates of significance and variance. Results: A hierarchy of simple models is used to design robust estimators meeting these goals for both stand alone and comparative experiments. This algorithm has been validated against an extensive panel of known spike experiments, and shows comparable performance to existing standards. Availability: Algorithms available commercially as part of the MAS 5.0 software package. Data sets available from the Affymetrix website. Contact: earl_hubbell@affymetrix.com Supplemental Information: http://www.affymetrix.com/community/publications/affymetrix/index.affx * To whom correspondence should be addressed.
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Hubbell et al. (2002) studied this question.