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:

Hi zoe.ward, 

For DEXSeq's vignette, this is documented in the section "4 Additional technical or experimental variables". Please let us know if something is not clear. Shortly, you need to pass the following formulae to both estimateDispersions and testForDEU:

formulaFullModel = ~ sample + exon + pair:exon + cond:exon
formulaReducedModel = ~ sample + exon + pair:exon

Alejandro 

In DRIMSeq, based on the design matrix, you would set the full model as

design_full <- model.matrix(~ cond + pair, data = samples(d))

and use it in dmPrecision() and dmFit().

In dmTest(), you can specify which coefficient you would like to test with coef = "condpre" or coef = "condpost", depending on which of the two conditions is as a reference. Or you could define the null model design matrix which would be

design_null <- model.matrix(~ pair, data = samples(d))

This is similar to the case with batches presented in the DRIMSeq vignette section 5.3 Differential transcript usage analysis between two conditions with accounting for the batch effects. In your case, patients are batches sort of.