TABLE 2

Posterior mean of residual variance, Embedded Image, regularization parameter, Embedded Image, and correlation between the true and estimated value for several items (Embedded Image, phenotypes; Embedded Image, true genomic value; Embedded Image, marker effects; all quantities averaged over 100 MC replicates)

Embedded ImageEmbedded ImageEmbedded ImageEmbedded ImageEmbedded Image
MeanaSDbMeanaSDbMeancSDbMeancSDbMeancSDb
Low linkage disequilibrium between markers (X0)
BL10.9090.08824.1101.8830.6400.0390.6570.0700.3280.062
BL20.9900.09535.9864.9440.6150.0440.6610.0730.3320.061
BL31.0350.09645.5066.7550.6010.0450.6600.0740.3290.059
BL41.0930.09863.7489.2000.5840.0440.6570.0770.3230.056
BL51.0060.10441.92011.5700.6100.0500.6600.0730.3300.059
High linkage disequilibrium between markers (X1)
BL10.9170.08823.7701.6210.6070.0390.6990.0710.2940.050
BL20.9910.09336.1684.1630.5690.0440.7050.0740.3000.046
BL31.0300.09545.5725.7350.5510.0450.7040.0760.2960.044
BL41.0780.09762.3738.4350.5290.0460.7000.0790.2910.043
BL51.0030.09941.0729.7240.5640.0510.7040.0740.2990.046
  • a Mean (across 100 MC replicates) of the posterior mean.

  • b Between-replicate standard deviation of the estimate.

  • c Mean (across MC replicates) of the correlation evaluated at the posterior mean of Embedded Image. The priors on Embedded Image were as follows: BL1, Embedded Image; BL2, Embedded Image; BL3, Embedded Image; and BL4, Embedded Image. In BL5, Embedded Image.