I'm trying to analyze an RNA-seq dataset that was just run. It consists of 3 conditions (Control, Treatment 1, Treatment 2) with 2 biological replicates (Cell line #1, Cell line #2) each. However, because the biological replicates are from cell lines of different passage number, there is variation in the base level of gene expression, even within the controls, making it difficult to conduct differential expression analysis across the replicates. For example, the expression value for the control of Cell line #1 may 1, but the control of cell line #2 may be 2. Thus, the expression values of the 2 treatments will vary accordingly, making it difficult to conduct edgeR analysis as there are a low number of differentially expressed genes with a FDR<0.05.
Is there a way to measure differential expression within each cell line individually? For example, is there a way to see which genes are differentially expressed between treatment 1 and the control for cell line #1, then seeing if these genes are also differentially expressed between treatment 1 and the control for cell line #2?
Thanks in advance.