Post-hoc filtering on the standard deviation in proportions
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Jack.Hearn • 0
@jackhearn-18689
Last seen 2.3 years ago

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

drimseq rnaseqdtu stager • 433 views
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@mikelove
Last seen 11 hours ago
United States

The first "rnaseqDTU" post!

Yes, you should put res.txp.filt$pvalue as the single column of pConfirmation, for performing stageR adjustment on the filtered transcript results.

If you want to see more of the original code it is here (with the relevant chunk highlighted):

https://github.com/mikelove/swimdown/blob/master/dtu/dtu_analysis.R#L75-L88

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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.

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Yes that’s what you would do

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