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

@article{citeulike:2627206, 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.}, author = {Lin, Shin and Carvalho, Benilton and Cutler, David J. and Arking, Dan E. and Chakravarti, Aravinda and Irizarry, Rafael A.}, citeulike-article-id = {2627206}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/gb-2008-9-4-r63}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18387188}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18387188}, day = {3}, doi = {10.1186/gb-2008-9-4-r63}, issn = {1465-6914}, journal = {Genome biology}, keywords = {affymetrix, bayesian, calling, snp}, month = {April}, number = {4}, pages = {R63+}, posted-at = {2009-10-23 14:19:08}, priority = {2}, title = {Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays.}, url = {http://dx.doi.org/10.1186/gb-2008-9-4-r63}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:2627206 L3 - citeulike-article-id:2627206 N2 - 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. IS - 4 JF - Genome biology SN - 1465-6914 TI - Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. VL - 9 SP - R63 KW - affymetrix KW - bayesian KW - calling KW - snp AU - Lin, Shin AU - Carvalho, Benilton AU - Cutler, David AU - Arking, Dan AU - Chakravarti, Aravinda AU - Irizarry, Rafael PY - 2008/04/03/ UR - http://dx.doi.org/10.1186/gb-2008-9-4-r63 ER -