Comment on: Legarra et al. Genetics Selection Evolution, 41:43
Alternative fast algorithm (Theo Meuwissen, 20 January 2009)
In the discussion section it is stated that ‘In simulations of breeding schemes and in cross-validation testing of GW-EBV, the large number of EBV evaluations required may make our fast algorithm the only means to implement BayesB type genome-wide breeding value estimation.’ However, an alternative fast and non-MCMC based algorithm, is published by VanRaden (2008). This algorithm uses a mixture of two normal distributions as a prior. Given this prior, approximate genomic EBVs are obtained by modifying the variance ratio for every SNP in the mixed model equations, which are, apart from the modified variance ratio, equal to the BLUP equations for SNP effects.<br><br>Theo Meuwissen<br><br>Reference:<br>VanRaden, PM (2008) Efficient Methods to Compute...
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Typo Table 1 (Andres Legarra, 12 November 2009)
A typo exists in Table 1. Correct pedigree is as follows:
1 0 0
2 0 0
3 0 0
4 1 2
5 3 2
6 3 2
7 4 5
8 4 5
Sorry for any inconvenient. I thank Ross Whetten for finding this out.
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Comment on: Legarra et al. Genetics Selection Evolution, 41:43
Alternative fast algorithm (Theo Meuwissen, 20 January 2009)
In the discussion section it is stated that ‘In simulations of breeding schemes and in cross-validation testing of GW-EBV, the large number of EBV evaluations required may make our fast algorithm the only means to implement BayesB type genome-wide breeding value estimation.’ However, an alternative fast and non-MCMC based algorithm, is published by VanRaden (2008). This algorithm uses a mixture of two normal distributions as a prior. Given this prior, approximate genomic EBVs are obtained by modifying the variance ratio for every SNP in the mixed model equations, which are, apart from the modified variance ratio, equal to the BLUP equations for SNP effects.<br><br>Theo Meuwissen<br><br>Reference:<br>VanRaden, PM (2008) Efficient Methods to Compute... read full comment
Comment on: Meuwissen et al. Genetics Selection Evolution, 41:2