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

Shin Lin, Benilton Carvalho, David J. Cutler, Dan E. Arking, Aravinda Chakravarti, Rafael A. Irizarry

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article numberR63
JournalGenome biology
Volume9
Issue number4
DOIs
StatePublished - Apr 3 2008

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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