I need your help to resolve this question, maybe is easy but I am new about it. I would be appreciated if give me please any idea about that.
actually, I have 8 sample (count file from HTSeq-count of RNA-seq data, with this order: D1_1, D1_2, D3_1, D3_2, R1_1, R1_2, R3_1, R3_2) and make them into 4 group (2 sample in each one). Now I am going to calculate the proportion of gene expression for each group. I have log scaled and normalized them, but I want to merge the ratio of gene expression of each 2 sample together (for ex D1_1 and D1_2) to do the next analysis. could you give me any advice to do that?
my dataset is like this:
D1_1 D1_2 D3_1 D3_2 ENSMUSG00000000001.4 1.39484378430357 2.46452589579488 2.15638312017686 1.39484378430357 ENSMUSG00000000003.15 0.211843606133756 0.360646924628625 0.307483505135223 0.211843606133756
but I want to have D1 (D1_1 and D1_2) versus D3 (D3_1 and D3_2). I need to merge or don't know should be gotten average or what else?
thanks in advance