I'm running an edgeR analysis on RNAseq data that was run in two seperate batches which I want to control for. Should the variable I'm interested in be first or last in the equation?
ie "design <- model.matrix(~group + batch)"
"design <- model.matrix(~batch + group)"?
The edgeR manual says the group should go last, similar to DESEeq2, but I have been told by a collegue that it should go first?