Table 3. Analysis of DEGs for MAQC2 and MAQC3 given a nominal FDR ≤ 0.05.
| Datasets | Methods | # of TP genes | # of FP genes | Actual FDR | PPV | SR | SPR |
|---|---|---|---|---|---|---|---|
| MAQC2 | DESeq | 363 | 59 | .140 | .860 | .931 | .609 |
| TMM | 377 | 97 | .204 | .797 | .967 | .358 | |
| FQ | 377 | 100 | .210 | .790 | .967 | .338 | |
| TC, Med & UQ | 376 | 101 | .212 | .788 | .964 | .331 | |
| Med-pgQ2 | 362 | 22 | .057 | .942 | .928 | .854 | |
| UQ-pgQ2 | 364 | 21 | .055 | .945 | .933 | .861 | |
| MAQC3 | DESeq | 385 | 105 | .214 | .786 | .990 | .271 |
| TMM | 385 | 98 | .203 | .797 | .990 | .319 | |
| TC, Med & UQ | 384 | 99 | .204 | .795 | .987 | .313 | |
| Med-pgQ2 & UQ-pgQ2 | 387 | 83 | .177 | .823 | .995 | .424 |
The number of true positive (TP) and the false positive (FP) genes, the actual false discovery rate (FDR), the positive predictive value (PPV), the sensitivity rate (SR) and specificity rate (SPR).