Table 1 The FDR and FNR of all methods for detecting DE genes in simulation studies. If the method failed to report any significant genes, the FDR was NA and FNR was 0.50 for scenario 1 and 0.09 for scenario 2
From: Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model
| Â | Â | Â | Setting 1 | Setting 2 | Setting 3 | |||
|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | FDR | FNR | FDR | FNR | FDR | FNR |
NBMM | Scenario 1 | 1 Rep | 0.00 | 0.00 | 0.00 | 0.17 | 0.00 | 0.14 |
| Â | Â | 3 Rep | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 |
| Â | Scenario 2 | 1 Rep | 0.07 | 0.00 | 0.00 | 0.02 | 0.21 | 0.02 |
| Â | Â | 3 Rep | 0.16 | 0.00 | 0.15 | 0.01 | 0.09 | 0.02 |
maSigPro | Scenario 1 | 1 Rep | 0.11 | 0.00 | 0.00 | 0.00 | NA | 0.50 |
| Â | Â | 3 Rep | 0.00 | 0.07 | 0.00 | 0.04 | NA | 0.50 |
| Â | Scenario 2 | 1 Rep | 0.00 | 0.00 | 0.00 | 0.00 | NA | 0.09 |
| Â | Â | 3 Rep | 0.00 | 0.01 | 0.00 | 0.01 | NA | 0.09 |
DyNB | Scenario 1 | 1 Rep | NA | 0.50 | 0.00 | 0.36 | NA | 0.50 |
| Â | Â | 3 Rep | 0.54 | 0.54 | 0.32 | 0.32 | 0.43 | 0.20 |
| Â | Scenario 2 | 1 Rep | NA | |||||
| Â | Â | 3 Rep | NA | |||||
edgeR | Scenario 1 | Rep 1 | NA | |||||
| Â | Â | 3 Rep | 0.50 | NA | 0.50 | NA | 0.50 | NA |
| Â | Scenario 2 | 1 Rep | NA | |||||
| Â | Â | 3 Rep | 0.88 | 0.00 | 0.00 | 0.00 | 0.86 | 0.00 |