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
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 | 0.7863 | 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 |