Data | Statistical test (package) | Methods | # of TP | # of FP | PPV | Actual FDR | Sensitivity | Specificity |
---|---|---|---|---|---|---|---|---|
MAQC2 (n = 2) | Exact test (edgeR) | UQ-pgQ2 | 377 | 22 | 0.945 | 0.055 | 0.967 | 0.851 |
TMM | 384 | 81 | 0.826 | 0.174 | 0.985 | 0.453 | ||
RLE | 380 | 91 | 0.807 | 0.193 | 0.974 | 0.385 | ||
UQ | 379 | 92 | 0.805 | 0.195 | 0.972 | 0.378 | ||
Wald test (DESeq2) | UQ-pgQ2 | 385 | 49 | 0.887 | 0.113 | 0.987 | 0.669 | |
UQ | 374 | 80 | 0.824 | 0.176 | 0.959 | 0.460 | ||
TMM | 374 | 82 | 0.820 | 0.180 | 0.959 | 0.446 | ||
RLE | 376 | 83 | 0.819 | 0.181 | 0.964 | 0.439 | ||
T-test (voom-limma) | UQ-pgQ2 & UQ | 363 | 76 | 0.827 | 0.173 | 0.931 | 0.487 | |
TMM | 373 | 97 | 0.794 | 0.206 | 0.956 | 0.345 | ||
RLE | 364 | 92 | 0.798 | 0.202 | 0.933 | 0.378 | ||
QL F-test (edgeR) | UQ-pgQ2 | 387 | 59 | 0.868 | 0.132 | 0.997 | 0.587 | |
TMM | 385 | 103 | 0.789 | 0.211 | 0.992 | 0.280 | ||
RLE & UQ | 385 | 108 | 0.781 | 0.219 | 0.992 | 0.245 | ||
MAQC3 (n = 5) | Exact test (edgeR) | UQ-pgQ2 | 383 | 51 | 0.882 | 0.118 | 0.987 | 0.643 |
TMM | 386 | 93 | 0.806 | 0.194 | 0.995 | 0.350 | ||
RLE | 386 | 98 | 0.798 | 0.202 | 0.995 | 0.315 | ||
UQ | 386 | 98 | 0.798 | 0.202 | 0.995 | 0.315 | ||
Wald test (DESeq2) | UQ-pgQ2 | 384 | 83 | 0.822 | 0.178 | 0.990 | 0.420 | |
UQ | 387 | 101 | 0.793 | 0.207 | 0.997 | 0.294 | ||
TMM | 386 | 103 | 0.789 | 0.211 | 0.995 | 0.280 | ||
RLE | 385 | 102 | 0.791 | 0.209 | 0.992 | 0.287 | ||
T-test (voom-limma) | UQ-pgQ2 & UQ | 362 | 58 | 0.862 | 0.138 | 0.932 | 0.594 | |
RLE | 376 | 64 | 0.856 | 0.146 | 0.969 | 0.552 | ||
TMM | 350 | 60 | 0.853 | 0.146 | 0.902 | 0.580 | ||
QL F-test (edgeR) | UQ-pgQ2 | 382 | 85 | 0.818 | 0.182 | 0.985 | 0.406 | |
TMM | 385 | 99 | 0.796 | 0.205 | 0.992 | 0.308 | ||
RLE | 386 | 105 | 0.786 | 0.214 | 0.995 | 0.267 | ||
UQ | 386 | 104 | 0.788 | 0.212 | 0.995 | 0.273 |