Study 2 | ||||||
---|---|---|---|---|---|---|
proportion | Method | Precision | Recall/TPR | FPR | F1 | Predicted DEG |
5% | iDEG | 0.957 (1.0\(\times 10^{-2}\)) | 0.733 (1.9\(\times 10^{-2}\)) | 0.002 (4.7\(\times 10^{-4}\)) | 0.83 (1.1\(\times 10^{-2}\)) | 766 (26) |
edgeR | 0.532 (1.1\(\times 10^{-2}\)) | 0.935 (7.7\(\times 10^{-3}\)) | 0.043 (1.9\(\times 10^{-3}\)) | 0.678 (9.0\(\times 10^{-3}\)) | 1760 (39) | |
DESeq | 1 (0) | 0.07 (3.6\(\times 10^{-2}\)) | 0 (0) | 0.131 (6.1\(\times 10^{-2}\)) | 70.35 (36) | |
DEGseq | 0.102 (9.0\(\times 10^{-4}\)) | 0.985 (3.9\(\times 10^{-3}\)) | 0.459 (4.4\(\times 10^{-3}\)) | 0.184 (1.5\(\times 10^{-3}\)) | 9699 (85) | |
10% | iDEG | 0.966 (8.2\(\times 10^{-3}\)) | 0.78 (1.9\(\times 10^{-2}\)) | 0.003 (8.2\(\times 10^{-4}\)) | 0.863 (9.7\(\times 10^{-3}\)) | 1616 (50) |
edgeR | 0.639 (8.8\(\times 10^{-3}\)) | 0.947 (5.2\(\times 10^{-3}\)) | 0.06 (2.3\(\times 10^{-3}\)) | 0.763 (6.8\(\times 10^{-3}\)) | 2966 (42) | |
DESeq | NA (NA) | 0 (0) | 0 (0) | NA (NA) | 0 (0) | |
DEGseq | 0.19 (1.6\(\times 10^{-3}\)) | 0.986 (2.8\(\times 10^{-3}\)) | 0.468 (4.5\(\times 10^{-3}\)) | 0.318 (2.3\(\times 10^{-3}\)) | 10394 (80) | |
15% | iDEG | 0.969 (5.1\(\times 10^{-3}\)) | 0.814 (1.5\(\times 10^{-2}\)) | 0.005 (8.3\(\times 10^{-4}\)) | 0.884 (7.7\(\times 10^{-3}\)) | 2519 (54) |
edgeR | 0.699 (7.2\(\times 10^{-3}\)) | 0.954 (4.1\(\times 10^{-3}\)) | 0.073 (2.5\(\times 10^{-3}\)) | 0.807 (5.2\(\times 10^{-3}\)) | 4098 (44) | |
DESeq | NA (NA) | 0 (0) | 0 (0) | NA (NA) | 0 (0) | |
DEGseq | 0.266 (2.1\(\times 10^{-3}\)) | 0.987 (2.1\(\times 10^{-3}\)) | 0.48 (5.0\(\times 10^{-3}\)) | 0.419 (2.6\(\times 10^{-3}\)) | 11128 (86) | |
20% | iDEG | 0.974 (4.2\(\times 10^{-3}\)) | 0.828 (1.5\(\times 10^{-2}\)) | 0.006 (1.0\(\times 10^{-3}\)) | 0.895 (7.8\(\times 10^{-3}\)) | 3402 (74) |
edgeR | 0.741 (6.0\(\times 10^{-3}\)) | 0.96 (3.2\(\times 10^{-3}\)) | 0.084 (2.6\(\times 10^{-3}\)) | 0.836 (4.1\(\times 10^{-3}\)) | 5182 (45) | |
DESeq | NA (NA) | 0 (0) | 0 (0) | NA (NA) | 0 (0) | |
DEGseq | 0.333 (2.3\(\times 10^{-3}\)) | 0.987 (1.9\(\times 10^{-3}\)) | 0.494 (5.0\(\times 10^{-3}\)) | 0.498 (2.6\(\times 10^{-3}\)) | 11858 (80) |
Study 3 | ||||||
---|---|---|---|---|---|---|
proportion | Method | Precision | Recall/TPR | FPR | F1 | Predicted DEG |
5% | iDEG | 0.926 (1.5\(\times 10^{-2}\)) | 0.652 (2.2\(\times 10^{-2}\)) | 0.003 (6.3\(\times 10^{-4}\)) | 0.765 (1.4\(\times 10^{-2}\)) | 704 (29) |
edgeR | 0.305 (6.3\(\times 10^{-3}\)) | 0.956 (6.0\(\times 10^{-3}\)) | 0.115 (3.4\(\times 10^{-3}\)) | 0.463 (7.3\(\times 10^{-3}\)) | 3133 (65) | |
DESeq | 0.999 (2.1\(\times 10^{-3}\)) | 0.152 (3.8\(\times 10^{-2}\)) | 0 (1.8e-05) | 0.262 (5.8\(\times 10^{-2}\)) | 152 (38) | |
DEGseq | 0.086 (6.7\(\times 10^{-4}\)) | 0.985 (3.9\(\times 10^{-3}\)) | 0.549 (3.9\(\times 10^{-3}\)) | 0.159 (1.2\(\times 10^{-3}\)) | 11409 (74) | |
10% | iDEG | 0.945 (1.1\(\times 10^{-2}\)) | 0.708 (2.2\(\times 10^{-2}\)) | 0.005 (1.1\(\times 10^{-3}\)) | 0.809 (1.2\(\times 10^{-2}\)) | 1500 (59) |
edgeR | 0.447 (6.2\(\times 10^{-3}\)) | 0.96 (4.3\(\times 10^{-3}\)) | 0.132 (3.3\(\times 10^{-3}\)) | 0.61 (6.0\(\times 10^{-3}\)) | 4296 (60) | |
DESeq | 1 (0) | 0 (5.2\(\times 10^{-4}\)) | 0 (0) | 0.002 (1.4\(\times 10^{-3}\)) | 1 (1) | |
DEGseq | 0.165 (1.1\(\times 10^{-3}\)) | 0.986 (2.5\(\times 10^{-3}\)) | 0.556 (4.2\(\times 10^{-3}\)) | 0.282 (1.6\(\times 10^{-3}\)) | 11975 (76) | |
15% | iDEG | 0.953 (7.0\(\times 10^{-3}\)) | 0.746 (1.6\(\times 10^{-2}\)) | 0.006 (1.1\(\times 10^{-3}\)) | 0.837 (9.1\(\times 10^{-3}\)) | 2349 (58) |
edgeR | 0.537 (5.7\(\times 10^{-3}\)) | 0.964 (3.7\(\times 10^{-3}\)) | 0.147 (3.4\(\times 10^{-3}\)) | 0.69 (4.8\(\times 10^{-3}\)) | 5384 (59) | |
DESeq | 1 (NA) | 0 (3.3e-05) | 0 (0) | 0.001 (NA) | 0 (0) | |
DEGseq | 0.235 (1.4\(\times 10^{-3}\)) | 0.986 (2.1\(\times 10^{-3}\)) | 0.565 (4.2\(\times 10^{-3}\)) | 0.38 (1.9\(\times 10^{-3}\)) | 12562 (73) | |
20% | iDEG | 0.962 (4.6\(\times 10^{-3}\)) | 0.763 (1.3\(\times 10^{-2}\)) | 0.008 (1.0\(\times 10^{-3}\)) | 0.851 (7.8\(\times 10^{-3}\)) | 3175 (64) |
edgeR | 0.602 (5.7\(\times 10^{-3}\)) | 0.966 (2.8\(\times 10^{-3}\)) | 0.16 (3.9\(\times 10^{-3}\)) | 0.742 (4.4\(\times 10^{-3}\)) | 6419 (64) | |
DESeq | NA (NA) | 0 (0) | 0 (0) | NA (NA) | 0 (0) | |
DEGseq | 0.299 (1.6\(\times 10^{-3}\)) | 0.986 (2.0\(\times 10^{-3}\)) | 0.577 (4.2\(\times 10^{-3}\)) | 0.459 (1.9\(\times 10^{-3}\)) | 13180 (68) |