Table 4

Bias* of genomic predictions from different methods, obtained for five traits of a mice population
Splitting Method Trait
W6W WGS BL %CD8+ CD4+/CD8+
Within POL −4% 1% −1% 1% 1%
emBayesB −62% 24% 2% −42% −52%
RR_GBLUP −9% 8% 13% 2% 4%
SS_BY −18% 22% - 5% 5%
SS_ABS −35% 4% −30% 5% 17%
RKHS −1% 1% −1% 1% 2%
SVR −4% 3% −6% 5% 4%
BayesCpi −26% 66% 81% −568% −91%
BayesC −43% 263% 69% −397% −420%
LASSO −85% 53% 2% −73% −73%
RF −1% 1% 1% 0% 1%
Across POL - - - - -
emBayesB −51% 5% 3% −58% −87%
RR_GBLUP −31% 8% 8% −2% 14%
SS_BY −44% 18% - −1% 17%
SS_ABS −54% −7% −38% −16% 31%
RKHS −23% 4% −4% 9% 10%
SVR −24% 6% −8% 14% 10%
BayesCpi −15% 83% 46% −719% −196%
BayesC 23% 280% 115% −239% −359%
LASSO −116% 40% 7% −70% −98%
RF −13% 2% −1% 5% 5%

*Average of ten replicates. Bias was measured as the average difference between observed and predicted phenotypes of testing set and is presented as a proportion of the standard deviation of each trait (in %). Trait = weight at 6 weeks (W6W), weight growth slope (WGS), body length (BL), percentage of CD8+ cells (%CD8+), ratio between CD4+ and CD8+ cells (CD4+/CD8+). Splitting= splitting strategy in cross-validation (within or across-family).

Neves et al.

Neves et al. BMC Genetics 2012 13:100   doi:10.1186/1471-2156-13-100

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