Table 3.
Median percent error (MPE) and 15% error fraction (EF.15) for gene expression levels inferred from 30 M reads of length 25 simulated assuming geometric isoform expression.
| Expression range | (0, 10-6] | (10-6, 10-5] | (10-5, 10-4] | (10-4, 10-3] | (10-3, 10-2] | All | |
|---|---|---|---|---|---|---|---|
| # genes | 120 | 5,610 | 11,907 | 1,632 | 102 | 19,372 | |
| Uniq | 37.4 | 43.6 | 42.7 | 43.0 | 48.2 | 43.0 | |
| Rescue | 32.8 | 28.7 | 26.0 | 25.1 | 28.8 | 26.7 | |
| MPE | GeneEM | 30.6 | 28.2 | 25.7 | 25.1 | 28.0 | 26.3 |
| Cufflinks | 33.0 | 21.1 | 19.0 | 20.2 | 40.2 | 19.7 | |
| RSEM | 23.6 | 11.0 | 7.2 | 7.9 | 11.4 | 8.1 | |
| IsoEM | 18.2 | 8.4 | 3.2 | 2.0 | 1.9 | 3.9 | |
| Uniq | 77.5 | 82.4 | 81.7 | 79.7 | 82.4 | 81.7 | |
| Rescue | 74.2 | 74.0 | 71.6 | 72.8 | 76.5 | 72.4 | |
| EF.15 | GeneEM | 72.5 | 73.8 | 71.5 | 73.0 | 74.5 | 72.3 |
| Cufflinks | 73.3 | 64.7 | 62.3 | 66.2 | 82.3 | 63.5 | |
| RSEM | 64.2 | 37.3 | 17.4 | 16.3 | 41.2 | 23.5 | |
| IsoEM | 57.5 | 28.1 | 6.7 | 6.1 | 4.9 | 13.2 | |