Hello,

I'm trying to create a design matrix using edgeR or DESeq2. I have a time course experiment with includes different does of a drug and different cell lines. For each cell line, I'd like to get DEGs for treated vs untreated but I am unsure of how to do this while taking the dose and time into account.

This is the metadata:

cell_line drug dose time

A untreated 0 0

A treated 1 2

A treated 1 6

A treated 1 24

A treated 1 48

A treated 3 2

A treated 3 6

A treated 3 24

A treated 3 48

B untreated 0 0

B treated 1 2

B treated 1 6

B treated 1 24

B treated 1 48

B treated 3 2

B treated 3 6

B treated 3 24

B treated 3 48

My general recommendation is to work with a statistician to settle on a statistical design and analysis plan. I only have time to provide software related support here.