@article{fc938d6472fc4b16a580dfd3d03fa1b3,
title = "Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays",
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.",
author = "Shin Lin and Benilton Carvalho and Cutler, {David J.} and Arking, {Dan E.} and Aravinda Chakravarti and Irizarry, {Rafael A.}",
note = "Funding Information: We would like to thank the Broad Institute and Affymetix for providing genotype data; Simon Cawley, Terry Speed, Earl Hubbell and Chuck Sugnet for helpful discussions; and finally, Ben Bolstad, James MacDonald, Seth Falcon, Marvin Newhouse, Robert Gentleman, Jiong Yang, and Fernando Pineda for help with hardware and software. The work of Rafael A Irizarry was partially funded by NIH grants 1R01GM083084-01, 1P41HG004059 and P50 HL73994 (Core E); Benilton Carvalho was funded by NIH grant 1R01RR021967-01A2 and Coordena{\c c}{\~a}o de Aperfei{\c c}oamento de Pessoal de N{\'i}vel Superior (CAPES/Brazil); Shin Lin, David J Cutler, Dan E Arking, and Aravinda Chakravarti were supported by NIH grants HG02757, MH60007, and the DW Reynolds Foundation. Note: Aravinda Chakravarti is a member of the Scientific Advisory Board of Affymetrix, Inc., a potential conflict of interest managed by the policies of Johns Hopkins University.",
year = "2008",
month = apr,
day = "3",
doi = "10.1186/gb-2008-9-4-r63",
language = "English (US)",
volume = "9",
journal = "Genome biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "4",
}