Table 3.
Comparison of number of significant genes using trait Q1
| α | SNP | GL | G2 | ||||||
|---|---|---|---|---|---|---|---|---|---|
| True | False | Total | True | False | Total | True | False | Total | |
| 1 × 10−5 | 1 | 2 | 3 | 2 | 1 | 3 | 1 | 3 | 4 |
| 1 × 10−4 | 1 | 4 | 5 | 2 | 6 | 8 | 1 | 4 | 5 |
| 1 × 10−3 | 2 | 19 | 21 | 2 | 23 | 25 | 1 | 12 | 13 |
| 0.01 | 2 | 73 | 75 | 3 | 101 | 104 | 1 | 75 | 76 |
| 0.10 | 4 | 389 | 393 | 5 | 397 | 402 | 4 | 303 | 307 |
| 0.25 | 5 | 718 | 723 | 6 | 695 | 701 | 7 | 626 | 633 |
| 0.50 | 6 | 1,266 | 1272 | 7 | 1,246 | 1,253 | 8 | 969 | 977 |
SNP, GL, and G2 are the SNP-based, gene-based linear, and gene-based two-step methods, respectively. The “True” columns are number of true associated genes; the “False” columns are number of false-positive genes; the “Total” columns are the total number of positive genes detected.