Table 1 Differential peak calling on simulated data
From: MMDiff: quantitative testing for shape changes in ChIP-Seq data sets
Profile changes | Â | |||||||
|---|---|---|---|---|---|---|---|---|
| Â | TP | FP | FN | TN | eFDR (%) | SN (%) | SP (%) | auROC (%) |
DESeq | 0 + 0.0 | 0.7 + 0.8 | 100 + 0.0 | 9799.3 + 0.8 | NaN | 0 + 0.0 | 100 + 0 | 50 + 0 |
DBChIP | 0.1 + 0.3 | 2.4 + 1.7 | 99.9 + 0.3 | 9797.6 + 1.7 | NaN | 0.1 + 0.3 | 100 + 0 | 50 + 0 |
DIME | 0 + 0.0 | 1.4 + 1.0 | 100 + 0.0 | 9798.6 + 1.0 | NaN | 0 + 0 | 100 + 0 | 50 + 0 |
GMD | 17.8 + 9.1 | 5.5 + 2.9 | 82.2 + 9.1 | 9794.5 + 2.9 | 26 + 10 | 17.8 + 9.1 | 99.9 + 0 | 83 + 0 |
MMDiff | 34.6 + 4.1 | 0.7 + 0.8 | 65.4 + 4.1 | 9799.3 + 0.8 | 2 + 0 | 34.6 + 4.1 | 100 + 0 | 83 + 0 |
Affinity changes | Â | |||||||
| Â | TP | FP | FN | TN | eFDR (%) | SN (%) | SP (%) | auROC (%) |
DESeq | 27.0 + 5.6 | 0.7 + 0.8 | 73.0 + 5.6 | 9799.3 + 0.8 | 2 + 0 | 27.0 + 5.6 | 100 + 0 | 81 + 0 |
DBChIP | 50.1 + 3.8 | 2.4 + 1.7 | 49.9 + 3.8 | 9797.6 + 1.7 | 4 + 0 | 50.1 + 3.8 | 100 + 0 | 94 + 0 |
DIME | 45.3 + 4.1 | 1.4 + 1.0 | 54.7 + 4.1 | 9798.6 + 1.0 | 3 + 0 | 45.3 + 4.1 | 100 + 0 | 95 + 0 |
GMD | 2.1 + 2.1 | 5.5 + 2.9 | 97.9 + 2.1 | 9794.5 + 2.9 | 73 + 30 | 2.1 + 2.1 | 99.9 + 0 | 60 + 10 |
MMDiff | 2.5 + 1.5 | 0.7 + 0.8 | 97.5 + 1.5 | 9799.3 + 0.8 | NaN | 2.5 + 1.5 | 100 + 0 | 70 + 0 |