Table 3 Average performance measures from a sensitivity analysis of the simulated gene expression data on 20 subjects (10 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 | FNR |
|---|---|---|---|---|
η=0.05 | ||||
LIMMA | 0.2111 | 0.5367 | 0.5328 | 0.2818 |
SAM | 0.6290 | 0.5879 | 0.7474 | 0.0625 |
SVA | 0.0445 | 0.9998 | 0.0405 | 0.0164 |
SVAPLS | 0.6408 | 0.9998 | 0.0029 | 0.0200 |
η=0.10 | ||||
LIMMA | 0.1953 | 0.5545 | 0.4871 | 0.2942 |
SAM | 0.5580 | 0.6079 | 0.7342 | 0.0606 |
SVA | 0.0239 | 0.9998 | 0.0514 | 0.0148 |
SVAPLS | 0.5125 | 0.9996 | 0.0077 | 0.0263 |
η=0.15 | ||||
LIMMA | 0.1900 | 0.5597 | 0.4838 | 0.3039 |
SAM | 0.5412 | 0.6126 | 0.7363 | 0.0600 |
SVA | 0.0190 | 0.9999 | 0.0395 | 0.0148 |
SVAPLS | 0.4544 | 0.9996 | 0.0112 | 0.0297 |