Table 6:

Simulation for SNP data (n, p) = (300, 505) under AR structures. 50 genes have nonzero regression coefficients. 5 clinical covariates are not subject to selection. The SNPs have AR structure with ρ = 0.5 (upper panel) and ρ = 0.8 (lower panel). mean(sd) of true positives (TP) and false positives (FP) based on 100 replicates.

		LAD_Network	LAD_MCP	LAD_LASSO	Network	MCP	LASSO
AR ρ = 0.5
Error1	TP	39.97(9.05)	39.77(3.54)	34.50(6.24)	33.50(6.60)	29.83(6.88)	46.03(2.30)
	FP	8.83(5.80)	9.33(7.71)	106.03(37.94)	9.13(6.26)	8.77(5.17)	84.53(11.25)
Error2	TP	23.23(10.57)	22.43(10.93)	27.43(8.64)	5.17(9.41)	6.93(14.32)	6.10(8.79)
	FP	23.93(40.56)	57.97(95.48)	110.17(66.55)	32.03(86.43)	45.67(126.72)	23.67(39.83)
Error3	TP	37.03(10.07)	36.17(4.53)	34.30(6.39)	16.17(11.50)	15.07(10.51)	28.30(16.74)
	FP	9.00(6.44)	15.93(26.06)	107.77(43.29)	8.50(5.76)	8.30(5.45)	58.40(34.86)
Error4	TP	38.13(7.35)	34.17(6.01)	34.90(7.04)	10.63(10.55)	9.83(9.89)	19.90(17.49)
	FP	10.17(6.86)	27.17(41.85)	109.70(45.23)	6.73(6.10)	6.07(6.49)	40.63(41.16)
AR ρ = 0.8
Error1	TP	46.87(5.11)	45.30(2.87)	42.87(6.06)	48.70(1.42)	26.07(3.49)	48.73(1.01)
	FP	3.80(2.96)	3.47(2.66)	104.20(30.42)	10.00(7.89)	6.67(3.39)	60.00(12.99)
Error2	TP	38.80(10.71)	26.17(6.93)	35.93(4.16)	5.97(10.07)	6.10(12.41)	5.70(7.53)
	FP	12.20(8.02)	44.20(83.64)	105.40(32.2)	35.30(89.14)	43.57(111.1)	25.77(42.43)
Error3	TP	46.70(6.02)	39.90(5.94)	43.17(3.65)	33.23(16.9)	18.10(9.78)	33.97(15.77)
	FP	6.77(5.88)	6.10(10.6)	105.63(28.03)	18.97(16.06)	20.83(65.59)	60.93(29.47)
Error4	TP	42.87(10.92)	36.03(6.83)	42.17(4.47)	25.93(16.99)	13.43(8.39)	29.33(15.39)
	FP	5.67(4.56)	10.30(21.71)	120.90(48.61)	19.77(13.39)	7.57(6.82)	50.30(31.1)