Extended Data Fig. 7: Differential expression analysis.
From: Joint probabilistic modeling of single-cell multi-omic data with totalVI
a, 2d density plot of totalVI and scVI log Bayes factors for genes. Bayes factors were computed for each gene in one-vs-all tests on the SLN111-D1 dataset. b, Number of isotype controls called differentially expressed in one-vs-all tests (n=27) for totalVI, totalVI-wBG (totalVI test without background removal), Wilcoxon rank-sum, and t-test. Tests were applied to SLN208-D1, for which isotype controls were retained. Box plots indicate the median (center lines), interquartile range (hinges), whiskers at 1.5x interquartile range. Red dashed line indicates the maximum number of isotype controls. c-e, Significance level (Bayes factors for totalVI, adjusted p-value for frequentist tests) for proteins in one-vs-all tests computed on SLN111-D1 and SLN111-D2 for each of (c) totalVI, (d) t-test, (e) Wilcoxon. f, Bayes factors for proteins in one-vs-all tests computed on the SLN111 datasets integrated with and without the SLN111-D2 proteins held-out. Differential expression tests for both model fits were conditioned on SLN111-D1. Bayes factors are colored by the average protein expression from SLN111-D1.
