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BioMed Central, Genome Biology, 4(9), p. R63

DOI: 10.1186/gb-2008-9-4-r63

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Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays

Journal article published in 2008 by Shin Lin, Benilton Carvalho, David J. Cutler, Dan E. Arking, Aravinda Chakravarti, Rafael A. Irizarry
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract Multiple algorithms have been developed for the purpose of calling single nucleotide polymorphisms (SNPs) from Affymetrix microarrays. We extend and validate the algorithm CRLMM, which incorporates HapMap information within an empirical Bayes framework. We find CRLMM to be more accurate than the Affymetrix default programs (BRLMM and Birdseed). Also, we tie our call confidence metric to percent accuracy. We intend that our validation datasets and methods, refered to as SNPaffycomp, serve as standard benchmarks for future SNP calling algorithms.