Table 2.
Average performance measures from a sensitivity analysis of the simulated gene expression data on 40 subjects (20 being in each group) under setting 1, with the four software packages limma, sam, sva and svapls
| Method | Sensitivity | Specificity | FDR | FNR |
|---|---|---|---|---|
|
η=0.05 | ||||
| LIMMA |
0.7863 |
0.2283 |
0.7719 |
0.5037 |
| SAM |
0.9793 |
0.5773 |
0.7724 |
0.0033 |
| SVA |
0.5659 |
0.9977 |
0.0475 |
0.0311 |
| SVAPLS |
0.9954 |
0.9998 |
0.0026 |
0.0003 |
|
η=0.10 | ||||
| LIMMA |
0.7577 |
0.2479 |
0.7432 |
0.5564 |
| SAM |
0.9854 |
0.6215 |
0.7055 |
0.0020 |
| SVA |
0.5695 |
0.9978 |
0.0471 |
0.0309 |
| SVAPLS |
0.9897 |
0.9994 |
0.0083 |
0.0008 |
|
η=0.15 | ||||
| LIMMA |
0.7307 |
0.2389 |
0.7464 |
0.5865 |
| SAM |
0.9816 |
0.6448 |
0.6609 |
0.0023 |
| SVA |
0.5393 |
0.9980 |
0.0443 |
0.0331 |
| SVAPLS | 0.9830 | 0.9990 | 0.0131 | 0.0012 |