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. Author manuscript; available in PMC: 2016 Jul 1.
Published in final edited form as: Ann Hum Genet. 2015 May 11;79(4):294–309. doi: 10.1111/ahg.12117

Table 4.

The number of SNPs truly and falsely associated with Q2 for GAW17 data with p-values less than different significance level α

1st 10th 100th 200th
SV LG oLG oPRB SV LG oLG oPRB SV LG oLG oPRB SV LG oLG oPRB
α TP FP TP FP TP FP TP FP TP FP TP FP TP FP TP FP TP FP TP FP TP FP TP FP TP FP TP FP TP FP TP FP
5×10−4 1 0 0 0 1 112 1 112 0 5 0 2 0 113 0 116 2 3 1 1 2 100 1 101 2 12 0 4 1 7 2 12
1×10−4 0 0 0 0 0 112 0 112 0 1 0 0 0 111 0 111 1 0 1 0 1 99 1 99 0 3 0 1 0 3 0 4
5×10−5 0 0 0 0 0 112 0 112 0 1 0 0 0 111 0 111 1 0 1 0 1 99 1 99 0 2 0 0 0 3 0 2
1×10−5 0 0 0 0 0 112 0 112 0 0 0 0 0 110 0 110 1 0 1 0 1 99 1 99 0 0 0 0 0 0 0 0

LG stands for logistic regression model on the regrouped binary outcome (recoding as 0 or greater than 0); SV stands for the set-valued method; coLG stands for ordered logistic regression method; oPRB is the usual probit model with IRWLS estimation algorithm. TP is the true positive; FP: the false positive;