Table 3

Empirical p-values estimated from 1000 permutations based on weighting score matrix 3.

q-value

Gene score


≥0.5

≥1

≥1.5

≥2

= 2.5


q < 0.9

0.393 (6399)

0.367 (1863)

0.603 (399)

0.191 (866)

0.052 (178)

q < 0.8

0.525 (469)

0.292 (415)

0.441 (163)

0.310 (199)

0.131 (108)

q < 0.7

0.495 (8)

0.228 (164)

0.627 (5)

0.208 (117)

0.118 (72)

q < 0.6

0.286 (5)

N/A

N/A

0.225 (42)

0.093 (53)

q < 0.5

0.113 (5)

N/A

N/A

0.122 (39)

N/A

q < 0.4

0.012 (5)

N/A

N/A

0.101 (27)

N/A


Based on Table 2, we used weight matrix 3 to rank genes (a total of 2458 genes) and then separated them according to their q-values. The number of SNPs in each q-value and score category based on COGA dataset is shown in parentheses. N/A: not available due to absence of the real data at those categories.

Zhao et al. BMC Genomics 2012 13(Suppl 8):S16   doi:10.1186/1471-2164-13-S8-S16

Open Data