Table 1. Results for select simulation settings, with parameters: n1, n2 (subpopulation sample sizes), d (gene length), μ (gene-level read depth) and ϕ (isoform-level dispersion). Parameter values n1, n2 = 50, 50; d = 1200; μ = 100; φ = 0.179 are treated as baseline, and deviations are marked by underlined values. For each setting, the numbers of significant calls out of 100 replications are reported for the default implementation of SigFuge, and DEXUS and SIBER at the gene, exon and 100bp levels of aggregation. The mean (standard deviation, SD) runtimes for single replications are reported in seconds for SigFuge, and DEXUS and SIBER at the 100bp level. Occasionally, NAs were reported in the output of SIBER. In this case, we mark the output with an asterisk (*m) and report the number of significant calls out of m < 100 simulations. For non-null simulations (settings 2, 3), the method with highest sensitivity is highlighted in bold. Complete simulation results may be found in Supplementary Table S3.
| Simulation parameters | SigFuge | DEXUS | SIBER | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Setting | n1, n2 | d |  |
 |
bp | Runtime (SD) | Gene | Exon | 100bp | Runtime (SD) | Gene | Exon | 100bp | Runtime (SD) |
| 1 | 100 | 1200 | 100 | 0.179 | 2 | 6.82 (0.31) | 0 | 0 | 1 | 0.58 (0.01) | 5 | 7 | 14 | 1.46 (0.26) |
| 1 | 100 | 1200 | 500 | 0.369 | 7 | 6.59 (0.18) | 0 | 2 | 2 | 0.58 (0.01) | 2 | 5 | 9 | 1.55 (0.31) |
| 1 | 20 | 1200 | 100 | 0.179 | 1 | 3.29 (0.14) | 17 | 48 | 79 | 0.16 (0.01) | – | – | – | – |
| 2 | 50, 50 | 1200 | 100 | 0.179 | 89 | 6.77 (0.23) | 0 | 13 | 21 | 0.60 (0.01) | 1 | 11 | 25 | 1.51 (0.26) |
| 2 | 75, 25 | 1200 | 100 | 0.179 | 98 | 6.86 (0.24) | 0 | 10 | 17 | 0.60 (0.03) | 2 | 16 | 21 | 1.47 (0.26) |
| 2 | 10, 10 | 1200 | 100 | 0.179 | 38 | 3.24 (0.12) | 23 | 76 | 86 | 0.17 (0.00) | – | – | – | – |
| 2 | 100, 100 | 1200 | 100 | 0.179 | 98 | 11.5 (0.21) | 0 | 0 | 0 | 1.16 (0.01) | 0 | 9 | 18 | 2.51 (0.40) |
| 2 | 50, 50 | 1200 | 100 | 0.087 | 100 | 6.71 (0.18) | 0 | 47 | 52 | 0.41 (0.02) | 3 | 86 | 91 | 1.08 (0.14) |
| 2 | 50, 50 | 1200 | 100 | 0.369 | 62 | 6.66 (0.18) | 0 | 10 | 16 | 0.40 (0.01) | 2 | 3 | 4*99 | 0.94 (0.22) |
| 3 | 50, 50 | 1200 | 100 | 0.179 | 99 | 6.82 (0.18) | 0 | 23 | 33 | 0.62 (0.11) | 3 | 26 | 38 | 1.50 (0.17) |
| 3 | 75, 25 | 1200 | 100 | 0.179 | 60 | 6.80 (0.19) | 0 | 56 | 72 | 0.61 (0.01) | 1 | 13 | 15 | 1.40 (0.19) |
| 3 | 10, 10 | 1200 | 100 | 0.179 | 29 | 3.25 (0.16) | 14 | 93 | 96 | 0.17 (0.00) | – | – | – | – |