Hello,

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)`

``

becomes

`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.

Best wishes,

Jack

Great, thanks for the swift reply! As a follow up I'm interested in contrasts from DRIMSeq so I assume the filtering and StageR steps need to be run for each contrast, that being the results of each "

`dmTest`

" performed.Yes that’s what you would do