Table 5

True and estimated effects for the simulated data with main and epistatic effects
locus i locus j True β EBLASSO- NE<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M85','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M85">View MathML</a> EBLASSO-NEG<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M86','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M86">View MathML</a> LASSO<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M87','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M87">View MathML</a> HyperLasso<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M88','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M88">View MathML</a> Two-locus test<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M89','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M89">View MathML</a>
11 11 1.99 0.83(0.12) 1.66(0.19) 0.72(0.65) 2.21(0.25) 0.88(0.10)
26 26 1.81 0.46(0.11) 1.42(0.18) 0.39(0.55) 1.73(0.23) 0.56(0.09)
42 42 −1.28 −0.36(0.11) −0.87(0.20) −1.59(0.21)b
48 48 −0.91 −0.19(0.09)b −0.68(0.19)b −0.14(0.55)b
72 72 1.28 1.01(0.16) 2.53(0.20) 0.92(1.18) 3.17(0.27) 1.08(0.10)
73 73 1.81 0.40(0.14) 1.04(0.10)
182 182 2.19 0.50(0.14) 1.57(0.26) 0.51(0.96) 2.03(0.30) 1.23(0.10)
185 185 1.29 0.69(0.14) 1.49(0.26) 0.57(0.91) 1.88(0.30) 1.23(0.10)
262 262 −1.28 −0.24(0.09) −0.70(0.15) −0.15(0.46) −0.78(0.19)b
268 268 0.91
5 6 1.28 0.42(0.13) 1.11(0.22) 0.40(0.63) 1.63(0.28)
6 39 1.29 0.38(0.15)b 1.37(0.23)b 0.15(1.16)b 1.28(0.35)b
42 220 1.99 0.23(0.13) 1.99(0.25)b 2.47(0.32) 0.77(0.14)
81 200 −1.28 −0.36(0.13)b −1.02(0.22)b −0.15(1.42)b −1.22(0.27)b
87 164 1.81 0.44(0.17) 1.73(0.25) 0.24(1.44) 2.15(0.32)b
87 322 2.19 0.90(0.15) 2.10(0.25) 0.74(0.66) 2.44(0.30) 0.79(0.13)
118 278 −1.28 −0.29(0.12) −0.76(0.20) −0.19(1.29) −0.99(0.26)
328 404 −0.99 −0.21(0.12)b −0.15(0.73)b −1.15(0.30)b
373 400 −0.91 −0.22(0.12)b −1.12(0.22)b −0.19(0.87) −1.23(0.27)
431 439 1.81 0.24(0.13) 1.37(0.24) 1.58(0.29)b
Parameter(s) λ = 0.1600 a = −0.2 λ=0.0254 a = 0.1
b = 0.1 α=0.01
CPU time(s) 2037.4 268.6 62.7 1094.6 2936.0
True/False positive 19/5c 17/4c 15/26c 17/7c 8/18d

aThe estimated marker effect is denoted by <a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M90','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M90">View MathML</a> and the standard deviation is denoted by <a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M91','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M91">View MathML</a>.

bThe estimated marker effect was obtained from a neighboring marker (≤ 20 cM) rather than from the marker with true effect.

cNumber of effects with p-value ≤ 0.05.

dNumber of effects with a p-value ≤ 4.31×10-7 after Bonferroni correction was applied.

Huang et al.

Huang et al. BMC Genetics 2013 14:5   doi:10.1186/1471-2156-14-5

Open Data