I am using DESe2 (v 1.33.4) to compare three shade avoidance phenotype in Arabidopsis.
I observed that the betaPrior in current version of DESeq2 was set to FALSE. If this is the case, we can compare C vs A and B vs A but we can't compare C vs B group.
When I tried setting the betaPrior to TRUE, I observed that I can get a group of A, B, C and I can make the three contrasts thereafter but I cannot use the lfcShrink function.
First question, how do you get the C vs B with betaPrior still set to FALSE and still be able to use the lfcShrink function?
Second question, if I want to detect WEAKLY EXPRESSED GENES between each group, would it be better to set the betaPrior into TRUE so I can ran the contrasts argument and alongside the lfcthreshold argument?
Then to shrink the CB effect, you can either use type="ashr" for shrinkage (easy), or for type="apeglm" you can do one extra step to make B the reference level and re-run just nbinomWaldTest() on the data to make C vs B one of the coefficients listed by resultsNames() (just two extra lines of code).
This is described in the "Extended section on shrinkage estimators" in the vignette.
What is a "weakly expressed gene between each group" I don't follow. Maybe give an example of what counts would look like.