Table 5

Inflation* 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 1.21 0.91 0.89 1.03 0.97
emBayesB 1.43 1.57 3.70 1.65 1.55
RR_GBLUP 0.95 0.70 0.88 0.66 0.75
SS_BY 0.79 0.66 - 0.60 0.72
SS_ABS 0.72 0.49 0.49 0.64 0.72
RKHS 1.08 0.95 0.89 1.06 1.26
SVR 1.24 0.91 0.68 1.16 1.18
BayesCpi 0.55 0.29 0.40 0.17 0.29
BayesC 0.18 0.12 0.21 0.19 0.20
LASSO 0.93 1.01 1.08 1.00 1.07
RF 1.48 1.10 0.78 1.12 1.11
Across POL - - - - -
emBayesB 0.46 0.90 1.47 1.43 1.33
RR_GBLUP 0.37 0.49 0.52 0.46 0.52
SS_BY 0.30 0.46 - 0.42 0.52
SS_ABS 0.29 0.30 0.32 0.50 0.52
RKHS 0.55 0.95 0.75 1.21 1.36
SVR 0.61 0.89 0.62 1.42 1.27
BayesCpi 0.22 0.21 0.14 0.17 0.24
BayesC 0.07 0.08 0.11 0.18 0.15
LASSO 0.38 0.71 0.56 0.98 1.01
RF 0.72 1.22 0.65 1.27 1.22

*Average of ten replicates. Inflation was measured as the slope of the regression of observed phenotypes on predicted phenotypes of testing set

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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