Table 3.

Non-convergence rate, analysis run time, and number of DEGs for 4 hypothesis tests in the shock dataset. 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%	0.04%	0%	0.31%	0%	4.33% (9.07%)	0.45%	0%
Analysis Time (minutes)
Model Fit Time	1.14	6.44	0.61	5.8	11.01	2.16	8.91	24.83	326.74	62.72	-
Total Time (Model Fit & Hypothesis Testing)	6.05	28.49	0.72	6.76	18.19	2.2	11.76	104.78	1450.86	65.6	415.12
Between Subject Test
SS vs. CS (Any timepoint)	5,323	-	5,179	-	4,034	3,801	3,009	3,303	3,633	3,351	3,461
Within Subject Tests
Change over time - SS group	5,252	8,331	5,155	8,319	7,910	9,796	8,048	8,600	7,772	8,281	8,081
Change over time - CS group	128	1,381	123	1,313	872	638	1,003	1,836	1,280	1,229	168
Interaction Test
Any Significant Interaction Effect	369	1,842	358	1,783	1,416	1,962	1,502	2,356	1,801	1,769	1,045