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. 2006 Aug;173(4):2269–2282. doi: 10.1534/genetics.106.058537

TABLE 1.

Comparison of the IM, HK, IRLS, and EE methods applied to simulated data under different strengths of epistasis

1:1:1
1:1:2
1:1:3
Mean SD MSE Mean SD MSE Mean SD MSE
μ = 0
IM 0.001 0.061 0.004 0.001 0.070 0.005 0.004 0.086 0.007
HK 0.000 0.063 0.004 0.001 0.074 0.006 0.003 0.091 0.008
IRLS 0.000 0.062 0.004 0.001 0.072 0.005 0.003 0.088 0.008
EE 0.000 0.062 0.004 0.001 0.072 0.005 0.002 0.088 0.008
a1 = 1
IM 0.998 0.136 0.019 0.995 0.164 0.027 1.018 0.181 0.033
HK 1.000 0.155 0.024 0.991 0.185 0.034 1.024 0.220 0.049
IRLS 1.001 0.152 0.023 0.993 0.181 0.033 1.024 0.212 0.046
EE 0.999 0.143 0.021 0.995 0.172 0.030 1.020 0.192 0.037
a2 = 1
IM 1.003 0.145 0.021 1.001 0.157 0.025 0.995 0.178 0.032
HK 1.003 0.160 0.026 1.003 0.178 0.032 1.000 0.215 0.046
IRLS 1.003 0.158 0.025 1.004 0.173 0.030 1.002 0.207 0.043
EE 1.004 0.151 0.023 1.003 0.163 0.027 0.996 0.188 0.035
b12
IM 0.987 0.289 0.084 2.005 0.342 1.128 2.986 0.395 4.101
HK 0.984 0.385 0.149 1.998 0.434 1.185 3.024 0.518 4.364
IRLS 0.984 0.385 0.148 1.997 0.433 1.182 3.024 0.517 4.364
EE 0.990 0.314 0.099 2.002 0.370 1.141 3.014 0.459 4.265
σ2
IM 0.548 0.073 0.006 0.731 0.092 0.009 1.026 0.127 0.018
HK 0.776 0.081 0.052 1.080 0.114 0.122 1.556 0.158 0.268
IRLS 0.560 0.091 0.008 0.751 0.131 0.017 1.035 0.187 0.036
EE 0.543 0.085 0.008 0.728 0.117 0.014 1.009 0.162 0.029
h2 = 0.5
IM 0.511 0.064 0.004 0.511 0.057 0.003 0.514 0.056 0.003
HK 0.426 0.062 0.009 0.414 0.063 0.011 0.416 0.065 0.011
IRLS 0.508 0.083 0.007 0.505 0.088 0.008 0.517 0.092 0.009
EE 0.514 0.075 0.006 0.513 0.074 0.006 0.522 0.075 0.006
LRT
IM 83.0 17.3 80.5 16.2 77.2 15.5
HK 73.6 16.4 65.1 14.7 61.3 14.4
IRLS 80.0 17.2 75.2 16.0 71.7 15.5
EE 80.6 17.2 75.8 16.0 72.3 15.5

For each combination of simulated parameters, 1000 replicates, each with sample size 200, were analyzed with QTL located in the middle of two unlinked 40-cM marker intervals. σ2 = 0.5625 for effect 1:1:1; σ2 = 0.75 for effect 1:1:2; σ2 = 1.0625 for effect 1:1:3. b12 = 1, 2, and 3 for the three effect ratios, respectively. h2, the broad sense heritability (proportion of variance explained by QTL).