Table 2. Type I error probabilities at significance levels of 5 × 10−2, 5 × 10−3, and 5 × 10−4.
| SNV (gompertz) | SNV (right tail+outliers) | |||
|---|---|---|---|---|
| (α=0.05) (α=0.005) (α=0.0005) | MAF=0.05 | MAF=0.005 | MAF=0.05 | MAF=0.005 |
| INT | 5.1e-02 5.2e-03 4.5e-04 | 5.0e-02 5.1e-03 5.3e-04 | 5.1e-02 5.2e-03 5.7e-04 | 5.0e-02 5.0e-03 4.3e-04 |
| WINS | NA | NA | 5.0e-02 4.9e-03 5.6e-04 | 4.9e-02 5.0e-03 5.3e-04 |
| DEL | NA | NA | 5.0e-02 4.9e-03 5.3e-04 | 5.0e-02 5.1e-03 4.4e-04 |
| IGNORE | 5.1e-02 5.1e-03 4.6e-04 | 4.9e-02 5.2e-03 6.7e-04 | 5.0e-02 5.5e-03 7.9e-04 | 4.8e-02 9.2e-03 2.6e-03 |
| PERM | 5.1e-02 5.1e-03 4.7e-04 | 4.9e-02 5.1e-03 5.8e-04 | 5.1e-02 5.1e-03 5.8e-04 | 5.0e-02 5.1e-03 4.1e-04 |
| LOG-NORM | 5.1e-02 5.1e-03 4.8e-04 | 4.9e-02 5.2e-03 6.7e-04 | 5.0e-02 5.2e-03 5.6e-04 | 4.8e-02 8.1e-03 1.9e-03 |
| K–W | 4.9e-02 4.7e-03 4.8e-04 | 4.5e-02 4.4e-03 4.8e-04 | 4.9e-02 5.0e-03 4.7e-04 | 4.6e-02 4.2e-03 3.2e-04 |
| HUBER | 5.1e-02 5.1e-03 6.1e-04 | 4.9e-02 5.2e-03 5.9e-04 | 5.0e-02 5.4e-03 6.3e-04 | 5.0e-02 5.7e-03 7.3e-04 |
Abbreviations: CMC, combined multivariate collapsing; DEL, deleting outliers; NA, not applicable; PLT, platelet counts; WBC, white blood cell counts; WINS, winsorising.
Results are shown for single-variant tests that were conducted for MAFs of 0.05 and 0.005. Results are shown for a left-tailed distribution that was simulated using the Gompertz distribution, as well as a right-tailed distribution (
) with outliers added. Inflated Type I error rates are highlighted in bold.