Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays.
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ABSTRACT:
SUBMITTER: Lin S
PROVIDER: S-EPMC2643934 | biostudies-literature | 2008 Apr
REPOSITORIES: biostudies-literature
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Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays.
Lin Shin S Carvalho Benilton B Cutler David J DJ Arking Dan E DE Chakravarti Aravinda A Irizarry Rafael A RA
Genome biology 20080403 4
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 stan ...[more]
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