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Table 1 Programs available for genotyping SNPs.

From: Genotyping and inflated type I error rate in genome-wide association case/control studies

Name Summary Statistic MM1 Data2 Data3 Notes
RLMM A , Θ B } No T M  
BRLMM 1 a s i n h ( 4 ) a s i n h ( 4 ( I A I B ) I A I B ) MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqaIXaqmaeaacqWGHbqyieGacqWFZbWCcqWFPbqAcqWFUbGBcqWFObaAcqGGOaakcqaI0aancqGGPaqkaaGccqWGHbqycqWFZbWCcqWFPbqAcqWFUbGBcqWFObaAdaqadaqcfayaamaalaaabaGaeGinaqJaeiikaGIaemysaK0aaSbaaeaacqWGbbqqaeqaaiabgkHiTiabdMeajnaaBaaabaGaemOqaieabeaacqGGPaqkaeaacqWGjbqsdaWgaaqaaiabdgeabbqabaGaeyOeI0IaemysaK0aaSbaaeaacqWGcbGqaeqaaaaaaOGaayjkaiaawMcaaaaa@4D79@ No E-U M Assumes genotypes in "training" data are known. "Training" data only uses high quality SNPs. Incorporates info from other SNPs as a B ayesian Prior.
CRLMM A+- ΘB+, ΘA-- ΘB-} No T L C orrects for the effect of total intensity level and probe length on {S ij } through more complex method, and allows corrections to vary by array.
CHIAMO { 1 n p k = 1 n p Y A k , 1 n p k = 1 n p Y A k } MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaaiWaaeaajuaGdaWcaaqaaiabigdaXaqaaiabd6gaUjabdchaWbaakmaaqadabaGaemywaK1aaSbaaSqaaiabdgeabjabdUgaRbqabaGccqGGSaaljuaGdaWcaaqaaiabigdaXaqaaiabd6gaUjabdchaWbaakmaaqadabaGaemywaK1aaSbaaSqaaiabdgeabjabdUgaRbqabaaabaGaem4AaSMaeyypa0JaeGymaedabaGaemOBa42aaSbaaWqaaiabdchaWbqabaaaniabggHiLdaaleaacqWGRbWAcqGH9aqpcqaIXaqmaeaacqWGUbGBdaWgaaadbaGaemiCaahabeaaa0GaeyyeIuoaaOGaay5Eaiaaw2haaaaa@5001@ Yes E-L, T* W CHIAMO is a Bayesian hierarchical mixture model and is greatly simplified by this brief summary
SNiPer-HD { R 1 , ... , R n p } ,  where R k = ( I P M A i j k ) / ( I P M A i j k + I P M B i j k ) MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@6662@ No E-U W Assumes genotypes in "training" data are unknown and requires the EM algorithm. "Training" data should only use high quality SNPs.
Moorhead 1 s i n h ( 2 ) s i n h ( I P M A + I P M B I P M B ) MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqaIXaqmaeaaieGacqWFZbWCcqWFPbqAcqWFUbGBcqWFObaAcqGGOaakcqaIYaGmcqGGPaqkaaGccqWFZbWCcqWFPbqAcqWFUbGBcqWFObaAdaqadaqcfayaamaalaaabaGaemysaK0aaSbaaeaacqWGqbaucqWGnbqtdaWgaaqaaiabdgeabbqabaaabeaacqGHRaWkcqWGjbqsdaWgaaqaaiabdcfaqjabd2eannaaBaaabaGaemOqaieabeaaaeqaaaqaaiabdMeajnaaBaaabaGaemiuaaLaemyta00aaSbaaeaacqWGcbGqaeqaaaqabaaaaaGccaGLOaGaayzkaaaaaa@4C3F@ N/A E-U W Originally for MIP, but applicable to Affymetrix. Plagnol demonstrated how to link genotype probabilities between cases and controls.
logiCALL { 1 s i n h ( 2 ) s i n h ( I P M A + I P M B I P M B ) , I P M A + I P M B } MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaqcfa4aaiWaaeaadaWcaaqaaiabigdaXaqaaGqaciab=nhaZjab=LgaPjab=5gaUjab=HgaOjabcIcaOiabikdaYiabcMcaPaaacqWFZbWCcqWFPbqAcqWFUbGBcqWFObaAdaqadaqaamaalaaabaGaemysaK0aaSbaaeaacqWGqbaucqWGnbqtdaWgaaqaaiabdgeabbqabaaabeaacqGHRaWkcqWGjbqsdaWgaaqaaiabdcfaqjabd2eannaaBaaabaGaemOqaieabeaaaeqaaaqaaiabdMeajnaaBaaabaGaemiuaaLaemyta00aaSbaaeaacqWGcbGqaeqaaaqabaaaaaGaayjkaiaawMcaaiabcYcaSiabdMeajnaaBaaabaGaemiuaaLaemyta00aaSbaaeaacqWGbbqqaeqaaaqabaGaey4kaSIaemysaK0aaSbaaeaacqWGqbaucqWGnbqtdaWgaaqaaiabdkeacbqabaaabeaaaiaawUhacaGL9baaaaa@58FA@ No E-L W-F Designed to lower false positive rate and assigns calls based on cumulative distribution, not density functions.
  1. 1Indicates use of mismatched probes
  2. 2Parameters were estimated by E xperimental or T raining data. For experimental data, under the null, cases and control genotype proportions could be L inked or U nlinked. * indicates optional.
  3. 3Distance can be M ahalanobis, W eighted Likelihood, or unweighted L ikelihood