Table 1. Summary results of differential abundance analyses using various methods.
| PERFORMANCE METRIC → METHOD ↓ |
No. of discoveries in absence of batch effects (total = 265) | No. of positive controls discovered in absence of batch effects (total = 8) | No. of discoveries in presence of batch effects (total = 265) | No. of positive controls discovered in presence of batch effects (total = 8) |
|---|---|---|---|---|
| t-tests | 49 | 5 | 24 | 2 |
| LIMMA | 115 | 6 | 19 | 4 |
| PCA-LIMMA | 158 | 5 | 119 | 7 |
| SVA-LIMMA | 152 | 7 | 114 | 7 |
| FAMT | 118 | 7 | 166 | 7 |
| RRmix | 39 | 6 | 42 | 7 |