Table 2.
Median percent error (MPE) and 15% error fraction (EF.15) for isoform expression levels inferred from 30 M reads of length 25 simulated assuming geometric isoform expression.
| Expression range | 0 | (0, 10-6] | (10-6, 10-5] | (10-5, 10-4] | (10-4, 10-3] | (10-3, 10-2] | All | |
|---|---|---|---|---|---|---|---|---|
| # isoforms | 13,290 | 10,024 | 23,882 | 18,359 | 1,182 | 66 | 66,803 | |
| Uniq | 0.0 | 100.0 | 98.4 | 97.1 | 98.5 | 96.6 | 95.4 | |
| Rescue | 0.0 | 294.7 | 75.5 | 49.2 | 30.4 | 28.3 | 71.9 | |
| MPE | UniqLN | 0.0 | 100.0 | 80.8 | 30.3 | 26.4 | 24.8 | 36.0 |
| Cufflinks | 0.0 | 100.0 | 49.7 | 25.5 | 27.2 | 44.6 | 34.1 | |
| RSEM | 0.0 | 100.0 | 31.9 | 13.5 | 11.4 | 13.0 | 21.2 | |
| IsoEM | 0.0 | 100.0 | 25.3 | 7.3 | 3.2 | 2.2 | 12.0 | |
| Uniq | 0.2 | 98.4 | 97.2 | 96.9 | 97.0 | 95.5 | 78.0 | |
| Rescue | 48.4 | 95.5 | 86.2 | 73.1 | 61.5 | 56.1 | 76.0 | |
| EF.15 | UniqLN | 0.2 | 97.2 | 86.2 | 82.8 | 83.3 | 77.3 | 69.8 |
| Cufflinks | 17.6 | 96.4 | 81.3 | 71.0 | 74.7 | 80.3 | 67.9 | |
| RSEM | 19.9 | 93.7 | 71.1 | 46.4 | 39.8 | 47.0 | 56.9 | |
| IsoEM | 3.4 | 93.1 | 65.1 | 29.1 | 11.1 | 7.6 | 46.1 | |