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

被引：26

作者：

Lin, Shin ^{[2
]}

Carvalho, Benilton ^{[1
]}

Cutler, David J. ^{[2
]}

Arking, Dan E. ^{[2
]}

Chakravarti, Aravinda ^{[1
,2
]}

Irizarry, Rafael A. ^{[1
]}

机构：

[1] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD 21205 USA

[2] Johns Hopkins Univ, Sch Med, McKusick Nathans Inst Genet Med, Baltimore, MD 21205 USA

来源：

GENOME BIOLOGY | 2008年 / 9卷 / 04期

关键词：

D O I：

10.1186/gb-2008-9-4-r63

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：12

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