Table 1

True and estimated effects for the simulated data with main effects
locus True β EBLASSO-NE<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M72','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M72">View MathML</a> EBLASSO-NEG<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M73','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M73">View MathML</a> LASSO<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M74','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M74">View MathML</a> HyperLasso<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M75','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M75">View MathML</a> BhGLM<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M76','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M76">View MathML</a> RVM<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M77','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M77">View MathML</a> Single QTL<a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M78','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M78">View MathML</a>
11 1.99 0.76(0.22) 1.61(0.22) 0.51(0.73) 1.67(0.30) 1.50(0.27) 3.87(0.60) 0.67(0.13)
26 1.81 0.54(0.19) 1.23(0.21) 0.93(0.38) 1.07(0.28) 1.53(0.47)b 0.73(0.13)
42 −1.28 −0.34(0.17) −0.72(0.21)b −1.02(0.29) −0.95(0.24)
48 −0.91 −0.40(0.19) −0.82(0.21) −1.12(0.28)b −0.91(0.23)
72 1.28 0.77(0.14)
73 1.81 1.37(0.21) 1.91(0.24) 1.03(0.85) 2.37(0.32) 2.16(0.28) 4.73(0.59) 0.80(0.14)
123 0.63
127 −0.63
161 0.44 0.30(0.15)b 0.59(0.19)b 0.82(0.25)b 1.15(0.35) 0.57(0.13)
181 0.99 0.38(0.20)b 1.67(0.18)
182 2.19 1.60(0.29) 2.86(0.31) 1.26(0.86) 3.34(0.38) −2.73(0.37) 5.01(0.72) 1.89(0.19)
185 1.29 0.36(0.17)b 0.56(0.19)b 0.27(0.43)b 1.00(0.27)b 0.73(0.32) 2.38(0.69)b 1.44(0.16)
221 −0.75 −0.36(0.16)b
243 −0.57 −0.34(0.15) −0.41(0.16) −0.26(0.33) −0.75(0.24) −0.69(0.20) −1.74(0.45)
262 −1.28
268 0.91 2.90(0.62)
270 0.57
274 −0.99 −1.90(0.46)b
361 0.41 0.30(0.16)b 0.40(0.16)b 0.15(0.56)b 0.77(0.24)b −0.72(0.21)b 1.80(0.40)b
461 0.51
Parameter(s) λ=0.050 a = 0.01 λ=0.0257 a = 0.1 <a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M81','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M81">View MathML</a>
b = 6 α=0.05
CPU time(s) 25.56 1.31 1.67 1.90 20.64 54.70 8.84
true/false positive 11/2c 11/1c 6/4c 10/1c 9/0c 17/18c 8/25d

aThe estimated marker effect is denoted by <a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M79','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M79">View MathML</a> and the standard deviation is denoted by <a onClick="popup('http://www.biomedcentral.com/1471-2156/14/5/mathml/M80','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/14/5/mathml/M80">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 a p-value ≤ 0.05.

dNumber of effects with a p-value ≤ 1.04×10-4 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