Table 4 Average performance measures from a sensitivity analysis of the simulated gene expression data on 40 subjects (20 being in each group) under setting 2, 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 | FDR |
|---|---|---|---|---|
η=0.05 | ||||
LIMMA | 0.5632 | 0.1690 | 0.8399 | 0.6629 |
SAM | 0.7845 | 0.6199 | 0.7158 | 0.0312 |
SVA | 0.1651 | 0.9993 | 0.0469 | 0.0329 |
SVAPLS | 0.8324 | 0.9998 | 0.0024 | 0.0111 |
η=0.10 | ||||
LIMMA | 0.5637 | 0.1640 | 0.8333 | 0.6967 |
SAM | 0.7378 | 0.6507 | 0.6471 | 0.0342 |
SVA | 0.1428 | 0.9994 | 0.0461 | 0.0331 |
SVAPLS | 0.7535 | 0.9995 | 0.0071 | 0.0165 |
η=0.15 | ||||
LIMMA | 0.5660 | 0.1619 | 0.8315 | 0.7183 |
SAM | 0.6983 | 0.6553 | 0.6481 | 0.0372 |
SVA | 0.1082 | 0.9995 | 0.0506 | 0.0350 |
SVAPLS | 0.6806 | 0.9995 | 0.0095 | 0.0211 |