Extended Figure 8. Reproducibility of estimates µ, σ², and α parameters.

(a–f) Reproducibility of estimated µ, σ², and α parameters between technical replicates. Scatter plots showing the relation between the estimated α (a), µ (b), and σ² (c) values for the two unstimulated/LPS 0h technical replicates. For µ (b) and σ² (c), estimates are plotted for all genes (leftmost), as well as (left to right) for genes only detected in more than 10, 20, 30, 40, or 50 cells, respectively. (d) – (f) show the same plots for the two LPS 4h technical replicates. (g–h) Reproducibility of estimated µ, σ², and α parameters between biological replicates. Scatter plots showing the relation between the α (g), µ (h), and σ² (i) values estimates for the two LPS 2h biological replicates. For µ (h) and σ² (i), estimates are plotted for all genes (leftmost), as well as (left to right) for genes only detected in more than 10, 20, 30, 40, or 50 cells, respectively. (j) – (l) show the same plots for the two LPS 4h biological replicates. (m,n) Relation between per-gene errors for µ, σ², and α and the number of cells in which the gene’s expression is detected, or its bulk expression level. Scatter plots displaying the differences in the σ² (left), µ (middle), and α (right) estimates for each gene between technical replicates for LPS 2h (m) or LPS 4h (n) (Y axis) as a function of either the number of cells in which the transcript is detected (X axis, for µ and σ²), or the transcript’s bulk expression level (TPM, X axis, for α). Notably, ò (left) estimates saturate (denoted by a magenta line and shaded box) after ~ 30 detectable events, while µ estimates saturate after ~ 10. Dashed orange line: 95% confidence interval. (o,p) Changes in µ, σ², and α between time points are significant as compared to null models from both technical and biological replicates. Shown are the cumulative distribution functions (CDF) for shifts in µ (left), σ² (middle), and α (right) between 2h and 4h (red CDF) for the “core” antiviral (top), “peaked” inflammatory (middle), and “sustained” inflammatory (bottom) modules compared to a null model (black CDF) derived from either technical (o) or biological (p) replicates (SI). In the vast majority of cases, the changes between time points are significant, as assessed by a Kolmogorov-Smirnof (KS) test (P-value of test in the upper left corner of each plot).