Table 2 Observed type I error rates for low nominal error rates
From: Linear models enable powerful differential activity analysis in massively parallel reporter assays
Nominal | edgeR | DESeq2 | QuASAR | mpralm | mpralm | FET | t-test |
|---|---|---|---|---|---|---|---|
error rate | Â | Â | Â | (agg) | (avg) | Â | Â |
Tewhey - large | Â | Â | Â | Â | Â | ||
1.62e-05 | 8.21e-04 | 8.22e-04 | 1.97e-03 | 1.64e-04 | NA | 2.82e-01 | 0 |
| Â | (5/6088) | (5/6084) | (12/6088) | (1/6088) | Â | (1718/6088) | (0/6088) |
1.03e-05 | 6.57e-04 | 8.22e-04 | 1.64e-03 | 0 | NA | 2.73e-01 | 0 |
| Â | (4/6088) | (5/6084) | (10/6088) | (0/6088) | Â | (1663/6088) | (0/6088) |
7.25e-06 | 4.93e-04 | 8.22e-04 | 1.64e-03 | 0 | NA | 2.66e-01 | 0 |
| Â | (3/6088) | (5/6084) | (10/6088) | (0/6088) | Â | (1618/6088) | (0/6088) |
6.25e-06 | 4.93e-04 | 6.57e-04 | 1.64e-03 | 0 | NA | 2.62e-01 | 0 |
| Â | (3/6088) | (4/6084) | (10/6088) | (0/6088) | Â | (1597/6088) | (0/6088) |
Tewhey - targeted | Â | Â | Â | Â | Â | ||
1.62e-05 | 5.71e-04 | 5.71e-04 | 1.71e-03 | 5.71e-04 | NA | 2.57e-02 | 0 |
| Â | (2/3503) | (2/3503) | (6/3503) | (2/3501) | Â | (90/3503) | (0/3503) |
1.03e-05 | 5.71e-04 | 5.71e-04 | 1.71e-03 | 5.71e-04 | NA | 2.37e-02 | 0 |
| Â | (2/3503) | (2/3503) | (6/3503) | (2/3501) | Â | (83/3503) | (0/3503) |
7.25e-06 | 5.71e-04 | 5.71e-04 | 1.43e-03 | 5.71e-04 | NA | 2.14e-02 | 0 |
| Â | (2/3503) | (2/3503) | (5/3503) | (2/3501) | Â | (75/3503) | (0/3503) |
6.25e-06 | 5.71e-04 | 5.71e-04 | 1.43e-03 | 5.71e-04 | NA | 2.00e-02 | 0 |
| Â | (2/3503) | (2/3503) | (5/3503) | (2/3501) | Â | (70/3503) | (0/3503) |
Inoue | Â | Â | Â | Â | Â | ||
1.62e-05 | 1.64e-03 | 2.05e-03 | 4.1e-04 | 0 | 4.1e-04 | 3.69e-03 | 4.1e-04 |
| Â | (4/2440) | (5/2440) | (1/2440) | (0/2440) | (1/2440) | (9/2440) | (1/2440) |
1.03e-05 | 1.64e-03 | 2.05e-03 | 4.1e-04 | 0 | 4.1e-04 | 3.28e-03 | 4.1e-04 |
| Â | (4/2440) | (5/2440) | (1/2440) | (0/2440) | (1/2440) | (8/2440) | (1/2440) |
7.25e-06 | 8.20e-04 | 2.05e-03 | 4.1e-04 | 0 | 4.1e-04 | 2.87e-03 | 4.1e-04 |
| Â | (2/2440) | (5/2440) | (1/2440) | (0/2440) | (1/2440) | (7/2440) | (1/2440) |
6.25e-06 | 8.20e-04 | 2.05e-03 | 4.1e-04 | 0 | 4.1e-04 | 2.46e-03 | 4.1e-04 |
| Â | (2/2440) | (5/2440) | (1/2440) | (0/2440) | (1/2440) | (6/2440) | (1/2440) |
Ulirsch | Â | Â | Â | Â | Â | ||
1.62e-05 | 0 | 0 | 1.09e-03 | 0 | 0 | 4.14e-01 | 0 |
| Â | (0/2756) | (0/2756) | (3/2756) | (0/2756) | (0/2756) | (1140/2756) | (0/2756) |
1.03e-05 | 0 | 0 | 7.26e-04 | 0 | 0 | 4.06e-01 | 0 |
| Â | (0/2756) | (0/2756) | (2/2756) | (0/2756) | (0/2756) | (1119/2756) | (0/2756) |
7.25e-06 | 0 | 0 | 7.26e-04 | 0 | 0 | 3.96e-01 | 0 |
| Â | (0/2756) | (0/2756) | (2/2756) | (0/2756) | (0/2756) | (1092/2756) | (0/2756) |
6.25e-06 | 0 | 0 | 7.26e-04 | 0 | 0 | 3.93e-01 | 0 |
| Â | (0/2756) | (0/2756) | (2/2756) | (0/2756) | (0/2756) | (1083/2756) | (0/2756) |
Shen | Â | Â | Â | Â | Â | ||
1.62e-05 | 2.45e-03 | 1.67e-02 | 2.98e-04 | 0 | 3e-04 | 7.39e-01 | 0 |
| Â | (8/3264) | (51/3052) | (1/3358) | (0/3286) | (1/3337) | (2412/3264) | (0/3264) |
1.03e-05 | 2.45e-03 | 1.54e-02 | 0 | 0 | 3e-04 | 7.33e-01 | 0 |
| Â | (8/3264) | (47/3052) | (0/3358) | (0/3286) | (1/3337) | (2393/3264) | (0/3264) |
7.25e-06 | 2.14e-03 | 1.31e-02 | 0 | 0 | 3e-04 | 7.30e-01 | 0 |
| Â | (7/3264) | (40/3052) | (0/3358) | (0/3286) | (1/3337) | (2384/3264) | (0/3264) |
6.25e-06 | 1.84e-03 | 1.21e-02 | 0 | 0e+00 | 0e+00 | 7.29e-01 | 0 |
| Â | (6/3264) | (37/3052) | (0/3358) | (0/3286) | (0/3337) | (2379/3264) | (0/3264) |