Entering edit mode
I know that for limma we use the following for when we have 2 control and 2 treated
design <- model.matrix(~c(rep(0,2),rep(1,2)))
and for Deseq2
condition <- factor(c("Control","Control","Treated","Treated"))
Now I have this questions one specifically for limma
1- does it matter in limma which design I use? for example if I have the frirst two column as control , should I assign them to 0 or 1?
2- what happens after enrichment analysis (how does the Deseq2 different from limma)?
actually one ignores the intercept and one involve the intercept . I am wondering which way is the right way to do ?
All the approaches described in Section 9.2 are correct and none of them "ignores" the intercept.
I'm not going to answer any more questions from you until you show some willingness to read the documentation. It would also be appreciated if you made a bit more effort to ask a better-formed question. At the moment, you don't seem to have an actual problem.