I have RNAseq read counts for three groups of sample, each with 3 replicates. I want to find the DE genes between Group 1 and Group 2, Group 2 and Group 3, and Group 1 and Group 3. Should I combine all the samples in one file and then perform the RUVs to normalize then get DE genes between two groups? OR should I make a separate file for each comparison group and then perform the RUVs on that group to normalize and get the DE genes?   

Thanks!