I have two different RNA-seq data from mouse; 1) paired-end read (40 bp) data of neonatal cardiac myocytes were dissociated from whole mouse hearts at 0, 4 and 7 days of birth with two replicates and 2) paired-end read (100 bp) data from the ventricular myocardium of mouse treated with factor X at 1th and 7 th days after birth with corresponding control with two replicates. I would like to get the differentially expressed genes between group 1 and group 2. Here is the MDS plot showing two distinct groups 1 and 2 at the right and left end of the graph:
Considering such a batch effect, could you please kindly tell me how I can include this batch effect in edgeR analysis?
Thank you in advance