Table 1 Performance of gene-level methods
Group | Method | Sensitivity (%) | Specificity (%) | False positives (%) | False negatives (%) |
|---|---|---|---|---|---|
Classical | Fisher | 59.18 | 88.64 | 5.89 | 40.82 |
Sidak | 18.37 | 97.73 | 0.11 | 81.63 | |
Simes | 46.94 | 97.73 | 1.33 | 53.06 | |
FDR | 24.49 | 97.73 | 0.13 | 75.51 | |
Updated Classical | TPM | 63.04 | 92.86 | 4.93 | 36.96 |
GATES | 24.49 | 98.00 | 0.17 | 75.51 | |
WGATES | 26.53 | 98.00 | 0.16 | 73.47 | |
HYST | 24.49 | 98.00 | 0.16 | 75.51 | |
WHYST | 24.49 | 98.00 | 0.16 | 75.51 | |
Novel | VEGAS | 20.41 | 100.0 | 0.16 | 79.59 |
VEGAS [10%] | 28.57 | 98.00 | 0.40 | 71.43 |