Table 3 Simulation for (n, p) = (500, 1500): mean(sd) of true positives (TP) and false positives (FP) based on 100 replicates. Upper panel: SNP data; Lower panel: gene expression data

AR

ρ = 0.1

TP

FP

48.52(12.31)

78.29(41.61)

37.57(12.59)

64.29(51.34)

57.55(14.03)

95.11(36.75)

46.60(14.58)

63.32(30.63)

AR

ρ = 0.5

TP

FP

126.91(10.98)

78.69(33.05)

59.37(10.48)

54.19(29.45)

92.57(6.94)

139.60(27.36)

78.83(6.70)

87.37(17.78)

AR

ρ = 0.9

TP

FP

148.43(9.83)

61.36(48.01)

47.82(12.45)

21.41(60.62)

105.29(5.34)

135.23(20.22)

80.05(4.81)

80.03(12.34)

Block

ρ = 0.1

TP

FP

67.16(12.67)

91.44(40.23)

52.23(11.89)

63.03(42.99)

81.51(7.92)

124.56(28.34)

70.51(7.25)

82.16(19.66)

Block

ρ = 0.5

TP

FP

146.63(7.27)

81.27(63.42)

57.24(13.70)

32.85(42.69)

105.11(4.96)

143.77(19.63)

89.64(4.46)

87.04(12.76)

Block

ρ = 0.9

TP

FP

143.11(5.33)

28.85(41.83)

43.92(10.42)

11.99(19.14)

105.69(5.16)

133.15(20.07)

82.12(5.11)

75.53(12.27)

AR

ρ = 0.1

TP

FP

47.41(10.56)

80.08(38.04)

45.27(11.08)

73.56(39.11)

61.12(12.18)

100.51(34.81)

49.37(13.06)

64.09(28.80)

AR

ρ = 0.5

TP

FP

137.85(9.22)

74.79(30.71)

50.61(9.79)

31.28(14.74)

96.19(6.07)

142.99(25.91)

81.23(5.95)

91.92(16.12)

AR

ρ = 0.9

TP

FP

148.80(3.65)

40.33(31.15)

38.57(9.09)

7.09(10.13)

107.95(4.73)

129.96(17.41)

70.91(4.23)

77.48(11.09)

Block

ρ = 0.1

TP

FP

60.37(11.61)

83.04(48.75)

53.43(12.30)

60.64(41.84)

86.67(6.85)

133.73(26.74)

74.79(5.96)

88.28(18.60)

Block

ρ = 0.5

TP

FP

140.67(14.14)

73.60(66.06)

53.89(13.26)

27.35(31.89)

104.83(4.67)

138.88(17.85)

86.65(4.25)

82.63(13.30)

Block

ρ = 0.9

TP

FP

145.12(5.00)

19.43(23.30)

33.07(7.61)

3.79(6.54)

106.67(5.81)

123.37(19.61)

64.76(4.71)

67.60(9.78)