I am following the "Swimming downstream" vignette for dtu using DRIMSeq and StageR and would like to clarify something. Does the output of section "5.3 Post-hoc filtering on the standard deviation in proportions" become the input for section "5.2 stageR following DRIMSeq" if performing the filtering? I think this is what is meant by "We do not recompute adjusted p-values, although we will provide the filtered p-values to the stageR procedure". With respect to section 5.2 of the vignette:
pConfirmation <- matrix(res.txp$pvalue, ncol=1)
pConfirmation <- matrix(res.txp.filt$pvalue, ncol=1)
Apologies for the minor point, but I want to be sure I'm understanding the vignette correctly.