I got a sample sheet like this:
name condition sampe1 T sampe2 T sampe3 N sampe4 T sampe5 N sampe6 N sampe7 N
When I use this condition in DEseq2, it will use N vs T as default.
If I set
group <- factor(c(1,1,2,1,2,2,2)) in EdgeR. It will get opposite result to DEseq2.
I would like to know. If I want to get the up-down regulated gene in Tumor sample.
Should I set tumor as "1" or "2" in EdgeR ?