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
From: svapls: an R package to correct for hidden factors of variability in gene expression studies
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 |