Variable Selection and Joint Estimation of Mean and Covariance Models with an Application to eQTL Data

Table 3

Comparisons of the performance of JMCCM with SCGGM, CAPME, and JML for models 1–6. Standard errors are presented in parenthesis.

Model	Method			SPE	SEN	Youden
1	JMCCM	0.139 (0.004)	0.519 (0.008)	0.864 (0.010)	0.723 (0.014)	0.587 (0.012)
	SCGGM	0.171 (0.007)	0.556 (0.010)	0.865 (0.030)	0.624 (0.027)	0.506 (0.014)
	CAPME	0.113 (0.003)	0.512 (0.008)	0.002 (0.001)	1.000 (0.000)	0.002 (0.001)
	JML	0.099 (0.003)	0.450 (0.005)	0.160 (0.026)	0.980 (0.005)	0.140 (0.024)
2	JMCCM	0.241 (0.005)	0.677 (0.009)	0.915 (0.004)	0.801 (0.007)	0.716 (0.006)
	SCGGM	0.349 (0.008)	0.821 (0.012)	0.661 (0.029)	0.882 (0.016)	0.542 (0.017)
	CAPME	0.430 (0.007)	1.028 (0.011)	0.005 (0.001)	1.000 (0.000)	0.005 (0.001)
	JML	0.232 (0.004)	0.670 (0.008)	0.210 (0.009)	0.980 (0.003)	0.200 (0.009)
3	JMCCM	0.705 (0.011)	1.145 (0.009)	0.947 (0.002)	0.653 (0.006)	0.600 (0.005)
	SCGGM	1.158 (0.034)	1.506 (0.032)	0.716 (0.036)	0.706 (0.029)	0.422 (0.010)
	CAPME	1.703 (0.012)	2.217 (0.015)	0.005 (0.000)	1.000 (0.000)	0.005 (0.000)
	JML	-	-	-	-	-
4	JMCCM	0.239 (0.006)	0.678 (0.011)	0.910 (0.004)	0.802 (0.007)	0.712 (0.007)
	SCGGM	0.402 (0.010)	0.869 (0.011)	0.825 (0.031)	0.772 (0.017)	0.597 (0.019)
	CAPME	0.447 (0.007)	1.081 (0.010)	0.004 (0.001)	1.000 (0.000)	0.004 (0.001)
	JML	0.284 (0.005)	0.793 (0.008)	0.110 (0.006)	1.000 (0.001)	0.100 (0.006)
5	JMCCM	0.463 (0.007)	0.953 (0.007)	0.941 (0.003)	0.731 (0.007)	0.672 (0.006)
	SCGGM	0.743 (0.011)	1.188 (0.010)	0.978 (0.002)	0.567 (0.007)	0.545 (0.007)
	CAPME	0.983 (0.008)	1.683 (0.012)	0.005 (0.001)	1.000 (0.000)	0.005 (0.001)
	JML	0.524 (0.524)	1.074 (0.009)	0.140 (0.006)	0.980 (0.002)	0.120 (0.006)
6	JMCCM	0.711 (0.010)	1.153 (0.010)	0.951 (0.002)	0.639 (0.006)	0.590 (0.005)
	SCGGM	1.126 (0.011)	1.438 (0.007)	0.988 (0.001)	0.440 (0.004)	0.428 (0.004)
	CAPME	1.781 (0.013)	2.406 (0.013)	0.006 (0.000)	0.999 (0.000)	0.006 (0.000)
	JML	-	-	-	-	-
1	JMCCM	0.068 (0.002)	0.364 (0.006)	0.814 (0.007)	0.886 (0.009)	0.700 (0.009)
	SCGGM	0.139 (0.010)	0.483 (0.018)	0.888 (0.024)	0.668 (0.031)	0.556 (0.016)
	CAPME	0.055 (0.002)	0.346 (0.006)	0.003 (0.001)	1.000 (0.000)	0.003 (0.001)
	JML	0.046 (0.001)	0.301 (0.005)	0.150 (0.015)	1.000 (0.001)	0.150 (0.015)
2	JMCCM	0.117 (0.003)	0.466 (0.006)	0.894 (0.003)	0.898 (0.005)	0.793 (0.004)
	SCGGM	0.168 (0.007)	0.550 (0.010)	0.652 (0.018)	0.960 (0.006)	0.612 (0.016)
	CAPME	0.215 (0.003)	0.696 (0.007)	0.003 (0.001)	1.000 (0.000)	0.003 (0.001)
	JML	0.119 (0.002)	0.459 (0.006)	0.320 (0.120)	0.990 (0.003)	0.310 (0.012)
3	JMCCM	0.321 (0.006)	0.766 (0.007)	0.916 (0.002)	0.808 (0.004)	0.724 (0.003)
	SCGGM	0.645 (0.015)	1.107 (0.011)	0.674 (0.021)	0.847 (0.024)	0.521 (0.008)
	CAPME	0.824 (0.006)	1.405 (0.007)	0.005 (0.000)	1.000 (0.000)	0.005 (0.000)
	JML	-	-	-	-	-
4	JMCCM	0.115 (0.003)	0.467 (0.006)	0.893 (0.003)	0.904 (0.006)	0.797 (0.005)
	SCGGM	0.286 (0.009)	0.745 (0.012)	0.786 (0.028)	0.822 (0.019)	0.609 (0.015)
	CAPME	0.215 (0.003)	0.703 (0.006)	0.003 (0.001)	1.000 (0.000)	0.003 (0.001)
	JML	0.123 (0.002)	0.486 (0.005)	0.160 (0.006)	1.000 (0.002)	0.150 (0.005)
5	JMCCM	0.217 (0.004)	0.643 (0.006)	0.924 (0.002)	0.867 (0.005)	0.792 (0.004)
	SCGGM	0.671 (0.011)	1.141 (0.001)	0.995 (0.002)	0.542 (0.009)	0.536 (0.008)
	CAPME	0.473 (0.004)	1.065 (0.007)	0.004 (0.000)	1.000 (0.000)	0.004 (0.000)
	JML	-	-	-	-	-
6	JMCCM	0.331 (0.005)	0.781 (0.006)	0.926 (0.002)	0.789 (0.005)	0.715 (0.004)
	SCGGM	1.024 (0.010)	1.380 (0.006)	0.998 (0.000)	0.414 (0.003)	0.412 (0.003)
	CAPME	0.844 (0.006)	1.466 (0.008)	0.005 (0.000)	0.999 (0.000)	0.004 (0.000)
	JML	-	-	-	-	-