Table 4.
Non-convergence rate, analysis run time, and number of DEGs for 4 hypothesis tests in the reduced shock dataset in which ten subjects from each group were randomly selected. The run time for fitting the full model for each gene, as well as the total time to fit models and perform hypothesis testing is displayed. There were 14,340 genes in the dataset and genes were labelled as a DEG if the Benjamini Hochberg adjusted p-value was < 0.05. For NBMM-LP, the percentage of genes in which one or more reduced models failed to converge is shown in parentheses after the full model non-convergence rate
| DESeq2 | DESeq2* | edgeR | edgeR* | GEE | limma | LMM | NBMM-AGQ | NBMM-LP | NBMM-PL | rmRNAseq | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| % Non-converged | 0% | 0% | 0% | 0% | 0.01% | 0% | 1.12% | 0.03% | 4.35% (9.07%) | 1.28% | 0% |
| Analysis Time (minutes) | |||||||||||
| Model Fit Time | 0.88 | 2.16 | 0.27 | 1.23 | 8.91 | 1.47 | 8.62 | 20.54 | 226.53 | 70.43 | - |
| Total Time (Model Fit & Hypothesis Testing) | 4.62 | 9.71 | 0.32 | 1.41 | 15.74 | 1.51 | 11.51 | 80.02 | 1067.07 | 73.26 | 327.84 |
| Between Subject Test | |||||||||||
| SS vs. CS (Any timepoint) | 4,201 | - | 3,337 | - | 3,108 | 1,743 | 1,387 | 2,422 | 2,290 | 1,696 | 1,355 |
| Within Subject Tests | |||||||||||
| Change over time - SS group | 1,684 | 4,466 | 1,397 | 3,960 | 4,875 | 5,894 | 3,925 | 5,124 | 4,390 | 4,323 | 2,994 |
| Change over time - CS group | 115 | 756 | 30 | 592 | 767 | 187 | 237 | 1,291 | 732 | 480 | 0 |
| Interaction Test | |||||||||||
| Any Significant Interaction Effect | 166 | 719 | 117 | 701 | 773 | 740 | 398 | 1,291 | 748 | 549 | 129 |