Table 4

Accuracy and bias of predicted GBVs evaluated with cross-validation in Data I
Method Trait A Trait B Trait C
MCBayes π = 0 rTBV,pGBV 0.832 ± 0.039 0.611 ± 0.095 0.501 ± 0.083
bTBV,pGBV 1.016 ± 0.022 1.072 ± 0.231 1.052 ± 0.341
ry,pGBV 0.741 ± 0.037 0.191 ± 0.045 0.160 ± 0.050
by,pGBV 1.013 ± 0.015 1.062 ± 0.125 1.039 ± 0.130
0 < π <1 rTBV,pGBV 0.791 ± 0.048 0.603 ± 0.112 0.390 ± 0.127
bTBV,pGBV 1.132 ± 0.064 1.210 ± 0.303 1.180 ± 0.379
ry,pGBV 0.705 ± 0.045 0.191 ± 0.046 0.121 ± 0.060
by,pGBV 1.131 ± 0.065 1.210 ± 0.170 1.119 ± 0.373
varBayes π = 0 rTBV,pGBV 0.813 ± 0.049 0.620 ± 0.108 0.470 ± 0.118
bTBV,pGBV 1.080 ± 0.048 0.994 ± 0.157 0.963 ± 0.201
ry,pGBV 0.722 ± 0.047 0.187 ± 0.056 0.143 ± 0.058
by,pGBV 1.072 ± 0.049 0.945 ± 0.195 0.931 ± 0.289
0 < π <1 rTBV,pGBV 0.779 ± 0.059 0.593 ± 0.111 0.423 ± 0.123
bTBV,pGBV 0.944 ± 0.040 0.816 ± 0.139 0.662 ± 0.153
ry,pGBV 0.690 ± 0.056 0.180 ± 0.055 0.125 ± 0.062
by,pGBV 0.935 ± 0.039 0.787 ± 0.166 0.626 ± 0.255
single-trait π = 0 rTBV,pGBV 0.826 ± 0.040 0.515 ± 0.073 0.505 ± 0.074
(MCBayes) bTBV,pGBV 0.997 ± 0.023 1.073 ± 0.270 1.030 ± 0.303
ry,pGBV 0.735 ± 0.039 0.159 ± 0.045 0.162 ± 0.044
by,pGBV 0.993 ± 0.012 1.071 ± 0.162 1.055 ± 0.222
0 < π <1 rTBV,pGBV 0.821 ± 0.039 0.531 ± 0.099 0.522 ± 0.094
bTBV,pGBV 1.131 ± 0.046 1.265 ± 0.555 1.192 ± 0.405
ry,pGBV 0.731 ± 0.037 0.164 ± 0.051 0.164 ± 0.048
by,pGBV 1.127 ± 0.043 1.249 ± 0.482 1.205 ± 0.457

Averages and standard errors evaluated with 10- fold cross-validation are listed based on 100 replicates of simulated data in Data I are listed for prediction accuracy, rpGBV,TBV, and bias, bpGBV,TBV, as well as correlation between phenotypic value and predicted GBV, ry,pGBV, and regression of phenotypic value on predicted GBV, by,pGBV , of each trait. For the settings of prior probability that a SNP has zero effect, π, see Table 1.

Hayashi and Iwata

Hayashi and Iwata BMC Bioinformatics 2013 14:34   doi:10.1186/1471-2105-14-34

Open Data