I have 12 samples from 2 different experiment. include D1,D3 (group D); R1,R3 (group R), Dnmt2ND1, Dnmt2ND2 (Dnmt2ND group), Dnmt2NF1, Dnmt2NF2 (Dnmt2NF), Dnmt2HD1, Dnmt2HD2 (Dnmt2HD group), Dnmt2HF1, Dnmt2HF2 (Dnmt2HF group). D and R groups are wild-type mice and Dnmt2 groups are Dnmt2-knocked-out mice. when I define all of them as gr and perform DE analysis no DEGs observed between D and R groups, but when I define D and R only as gr (without any Dnmt2 groups) tehn perform DE analysis for D and R, DEG sobserved (many genes can be up and down regulated). does anybody have any idea about this conflict that I face with?
thanks in advance