I did two batches of RNA-seq upon same drug treatment but at different time points on the same cell line. For each time point, I have corresponding DMSO controls. All my Fold Change values are calculated over the corresponding DMSO control. I'm trying to trace the gene expression dynamics upon my drug treatment. I found that if I simply merge two datasets into one master table and plot the RPKM and Fold Change values, the numbers do not reflect the real dynamics I saw by q-PCR. For example: I knew one gene (and a few more) that can be induced highest upon 4-day treatment but the RPKM values and Fold Changes do not show the same trend. So my question is:
What's the best way to address this issue?
Appreciate your help.