Table 4.
Standard deviation of total discoveries across six DNA methylation differential analysis methods using β values for independent case
| n | π 1 | Standard deviation of total discoveries | ||||||
|---|---|---|---|---|---|---|---|---|
| Rank test | t-test | KS test | Permutation | Empirical Bayes | Bump hunting BH | Bump hunting q-value | ||
| 3 | 0.01 | 0 | 0.39 | 0 | 0 | 1.02 | 0.87 | 1.03 |
| 0.05 | 0 | 1.14 | 0 | 0 | 4.79 | 3.09 | 3.80 | |
| 0.10 | 0 | 2.48 | 0 | 0 | 6.67 | 6.2 | 7.45 | |
| 0.25 | 0 | 7.87 | 0 | 0 | 9.71 | 11.65 | 15.38 | |
| 0.50 | 0 | 18.97 | 0 | 0 | 12.78 | 17.29 | 24.73 | |
| 0.75 | 0 | 25.68 | 0 | 0 | 14.73 | 19.56 | 35.22 | |
| 0.90 | 0 | 26.8 | 0 | 0 | 14.82 | 19.28 | 42.44 | |
| 6 | 0.01 | 0.00 | 1.61 | 0.00 | 0.00 | 1.30 | 1.67 | 1.70 |
| 0.05 | 0.00 | 4.05 | 0.00 | 0.00 | 2.95 | 3.68 | 3.69 | |
| 0.10 | 4.44 | 5.22 | 4.44 | 4.44 | 4.02 | 4.8 | 5.13 | |
| 0.25 | 12.17 | 7.04 | 7.04 | 8.83 | 6.02 | 6.93 | 8.03 | |
| 0.50 | 9.47 | 9.42 | 9.73 | 9.01 | 7.94 | 9.08 | 12.65 | |
| 0.75 | 9.90 | 9.82 | 8.55 | 10.48 | 8.65 | 9.39 | 21.72 | |
| 0.90 | 10.73 | 10.28 | 9.10 | 10.77 | 9.05 | 9.84 | 25.79 | |
| 12 | 0.01 | 1.41 | 1.03 | 1.02 | 0.00 | 0.99 | 1.10 | 1.11 |
| 0.05 | 3.01 | 2.21 | 2.14 | 2.46 | 2.22 | 2.33 | 2.39 | |
| 0.10 | 3.32 | 3.09 | 2.66 | 3.58 | 3.11 | 3.21 | 3.42 | |
| 0.25 | 5.26 | 4.48 | 3.65 | 5.08 | 4.35 | 4.70 | 5.42 | |
| 0.50 | 5.16 | 5.53 | 4.28 | 5.66 | 5.30 | 5.71 | 9.26 | |
| 0.75 | 5.07 | 5.70 | 3.83 | 5.76 | 5.37 | 5.70 | 14.69 | |
| 0.90 | 5.51 | 5.60 | 3.46 | 5.47 | 4.95 | 5.56 | 20.73 | |
| 24 | 0.01 | 0.96 | 0.77 | 0.71 | 0.00 | 0.85 | 0.87 | 0.91 |
| 0.05 | 1.87 | 1.64 | 1.23 | 1.79 | 1.76 | 1.76 | 1.82 | |
| 0.10 | 2.42 | 2.30 | 1.98 | 2.70 | 2.38 | 2.40 | 2.62 | |
| 0.25 | 3.21 | 3.17 | 2.92 | 3.75 | 3.22 | 3.26 | 4.15 | |
| 0.50 | 3.89 | 3.78 | 2.38 | 3.93 | 3.74 | 3.85 | 7.08 | |
| 0.75 | 2.99 | 3.29 | 2.57 | 3.45 | 3.25 | 3.31 | 12.30 | |
| 0.90 | 2.24 | 2.71 | 1.77 | 2.80 | 2.66 | 2.72 | 19.26 | |