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).