Table 1.
Average performance measures from a sensitivity analysis of the simulated gene expression data on 20 subjects (10 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 |
0.2287 |
0.6276 |
0.4285 |
0.2089 |
| SAM |
0.9239 |
0.6066 |
0.7278 |
0.0125 |
| SVA |
0.3311 |
0.9987 |
0.0475 |
0.0456 |
| SVAPLS |
0.9464 |
0.9998 |
0.0023 |
0.0039 |
|
η=0.10 | ||||
| LIMMA |
0.2307 |
0.6566 |
0.3724 |
0.2295 |
| SAM |
0.8880 |
0.6410 |
0.6596 |
0.0147 |
| SVA |
0.2882 |
0.9988 |
0.0481 |
0.0469 |
| SVAPLS |
0.9098 |
0.9994 |
0.0076 |
0.0065 |
|
η=0.15 | ||||
| LIMMA |
0.1956 |
0.6672 |
0.3689 |
0.2164 |
| SAM |
0.8522 |
0.6709 |
0.6140 |
0.0193 |
| SVA |
0.2474 |
0.9990 |
0.0458 |
0.0485 |
| SVAPLS | 0.8660 | 0.9991 | 0.0130 | 0.0097 |