Hello,

I am using DEXSeq to test for differential transcript usage across age and brain region in mouse. I have 10 young and 10 old mice, each profiled across 8 anatomical regions.

Each sample is defined by mouse ID × region, and my current full model is:

~ sample + exon + group:exon

where group = <age>_<region>.

The reduced model I use is:

~ sample + exon

This tests for any usage differences across groups, but I would like to test age effects within each region without subsetting the data and rerunning DEXSeq separately for each region. Is there a recommended way in DEXSeq to do this using contrasts or appropriate full/reduced models within a single fitted object?

Thank you for your guidance!