I have 85 paired samples i.e. before and after ischemia so my question is how would I run the DEXSeq and DRIMSeq on paired samples? I’ve had a look in the relevant vignettes but cannot find any example of paired analysis.
I have a design matrix like so:
One note about the rnaseqDTU workflow is that I initially made an error and included nbinomLRT() in the DEXSeq code. This should be testForDEU(). The workflow code on Bioconductor and on F1000Research has now been fixed to show testForDEU().