Table 2 The empirical Type I error rates (× 100) and power (× 100) of the six tests when methylation values were generated from Beta distributions. The numbers of non-diseased and diseased samples are (100, 100)
From: Robust joint score tests in the application of DNA methylation data analysis
Scenarios | Outlier | α(%) | jointLRT | KS | AW | iAW.Lev | iAW.BF | iAW.TM |
|---|---|---|---|---|---|---|---|---|
eqM&eqV | No | 5 | 5.7 | 3.5 | 5.4 | 5.4 | 5.4 | 5.5 |
(Type I error) | No | 1 | 1.5 | 0.5 | 1.0 | 1.1 | 1.2 | 1.1 |
No | 0.5 | 0.8 | 0.3 | 0.5 | 0.5 | 0.5 | 0.5 | |
diffM&eqV | No | 5 | 96.8 | 94.7 | 97.5 | 97.2 | 97.4 | 97.4 |
No | 1 | 88.4 | 86.7 | 91.7 | 90.5 | 91.0 | 90.9 | |
No | 0.5 | 83.1 | 77.5 | 87.8 | 86.6 | 87.9 | 87.4 | |
eqM&diffV | No | 5 | 88.1 | 18.9 | 86.8 | 83.1 | 82.7 | 83.0 |
No | 1 | 68.6 | 6.2 | 65.8 | 62.2 | 60.6 | 61.3 | |
No | 0.5 | 60.4 | 2.5 | 55.6 | 53.5 | 52.6 | 53.2 | |
diffM&diffV | No | 5 | 83.5 | 64.5 | 88.6 | 84.9 | 85.8 | 85.9 |
No | 1 | 58.1 | 42.8 | 70.4 | 63.0 | 64.5 | 64.8 | |
No | 0.5 | 48.9 | 30.2 | 60.6 | 54.6 | 57.6 | 56.8 | |
eqM&eqV | Yes | 5 | 11.0 | 3.6 | 3.8 | 5 | 4.9 | 4.9 |
(Type I error) | Yes | 1 | 3.3 | 0.6 | 0.7 | 1.0 | 1.0 | 1.0 |
Yes | 0.5 | 1.8 | 0.3 | 0.3 | 0.5 | 0.5 | 0.5 | |
diffM&eqV | Yes | 5 | 97.6 | 95.9 | 98.8 | 98.6 | 98.8 | 98.7 |
Yes | 1 | 89.2 | 87.7 | 94.8 | 93.4 | 94.0 | 93.7 | |
Yes | 0.5 | 82.6 | 79.6 | 91.6 | 89.3 | 89.9 | 89.8 | |
eqM&diffV | Yes | 5 | 31.9 | 15.7 | 24.9 | 61.2 | 59.8 | 60.6 |
Yes | 1 | 11.5 | 5.1 | 6.7 | 33.0 | 31.3 | 32.1 | |
Yes | 0.5 | 6.6 | 2.0 | 4.0 | 23.2 | 21.3 | 22.0 | |
diffM&diffV | Yes | 5 | 26.4 | 59.9 | 36.6 | 52.6 | 53.4 | 53.6 |
Yes | 1 | 8.4 | 38.3 | 15.4 | 24.9 | 25.7 | 25.5 | |
Yes | 0.5 | 4.5 | 26.0 | 10.6 | 16.5 | 17.2 | 17.2 |