Journal
GENOME BIOLOGY
Volume 9, Issue 4, Pages -Publisher
BMC
DOI: 10.1186/gb-2008-9-4-r63
Keywords
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Funding
- NCRR NIH HHS [R01 RR021967, 1R01RR021967-01A2, R01 RR021967-02] Funding Source: Medline
- NHGRI NIH HHS [HG02757, 1P41HG004059, U54 HG002757, P41 HG004059] Funding Source: Medline
- NHLBI NIH HHS [P50 HL73994, P50 HL073994] Funding Source: Medline
- NIGMS NIH HHS [R01 GM083084-02, R01 GM083084, R01 GM083084-01, 1R01GM083084-01] Funding Source: Medline
- NIMH NIH HHS [R01 MH060007, MH60007] Funding Source: Medline
- NATIONAL CENTER FOR RESEARCH RESOURCES [R01RR021967] Funding Source: NIH RePORTER
- NATIONAL HEART, LUNG, AND BLOOD INSTITUTE [P50HL073994] Funding Source: NIH RePORTER
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [P41HG004059, U54HG002757] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM083084] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF MENTAL HEALTH [R01MH060007] Funding Source: NIH RePORTER
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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.
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