I have RNA-seq data for four time points (spaced unequally), A B C and D. I have done both a spline and a group model to look for overall changes over time and between timepoints.
Is there a way of testing whether the amount of up- or downregulation is different between A/B and B/C or C/D (e.g. whether there is more upregulation between earlier timepoints)? Is sum(log2FC), separate for up and downregulated genes, the best way of expressing this?
I know it is possible that a lowly-expressed gene can change its expression slightly and produce a big log2FC, distorting the data; thus I'm also looking at the number of changing genes (first plot) and the number of counts underlying these changes (third plot).
e: I assume I can use the Chi2 test to examine the number of changing genes (first plot), and possibly the Mann-Whitney-U test to compare the amount of counts (third plot), but I am unsure which test would be appropriate for the second.