I am new to limma so please excuse my ignorance.
I am trying to use limma-voom to compare the effect of a treatment between males and females from an rna-seq experiment. I have paired samples, and my data looks as such:
I setup my design as such: design = model.matrix(~ sex + sex:nested + sex:condition, data), and then did fit <- lmFit(v, design) in accordance with the manual.
I'm confused as to how best proceed to make a contrast matrix that compares the effect of the condition between the sexes while accounting for the pairing. Any help would be much appreciated!