readme.pcgtest
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If the program does not converge with many rounds, it is would be better to reconsider the model, (co)variance components, the data used. | If the program does not converge with many rounds, it is would be better to reconsider the model, (co)variance components, the data used. | ||
< | < | ||
- | OPTION blksize | + | OPTION blksize |
</ | </ | ||
- | Set block size for preconditioner (default 1). | + | Set block size for preconditioner (default |
- | For a model with correlated random effects such as maternal effect models, random regression models, " | + | For a model with multiple trait with n traits |
+ | |||
+ | For a model with a single trait but correlated random effects such as maternal effect models, random regression models, " | ||
+ | |||
+ | For the case of a multiple trait model with correlated random effects use '' | ||
< | < | ||
OPTION init_eq 10 | OPTION init_eq 10 | ||
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//For information on availability of BLUP90IOD3, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.// | //For information on availability of BLUP90IOD3, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.// | ||
+ | |||
+ | ===== Tips for running BLUP90IOD3 ===== | ||
+ | When the convergence is very slow or never reached, there are several reasons. One of the major issues is the left-hand-side in MME is close to non-positive definite. | ||
+ | |||
+ | 1. The covariance matrix G and/or R is close to non-positive definite.\\ | ||
+ | In this case, change the tolerance value (xx) in the option: | ||
+ | |||
+ | OPTION tol xx | ||
+ | |||
+ | to a lenient value (e.g., 1d-04), | ||
+ | |||
+ | which is similar to re-parameterization for G = VDV' using larger eigenvalue(s) in D. | ||
+ | |||
+ | 2. Use " | ||
+ | |||
+ | 3. Remove the old data, which the contribution to the current active population is minimal. | ||
+ | |||
+ | 4. Remove non-contribution animals, which have no relationships with other animals that have phenotypes. | ||
+ | |||
+ | 5. Re-estimate the variance-covariance matrices accurately using the current data. | ||
+ | |||
+ | 6. Remove animals with no phenotypes in the input data file. If those animals have relationships in the pedigree and/or the genotypes, they will be included in the renaddXX.ped (output pedigree file) after running renumf90. So, they do not need to be included in the phenotypic data file when they have no phenotypes. | ||
+ | |||
+ | :\\ | ||
+ | : | ||
+ | |||
readme.pcgtest.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1