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
Cross-posted: https://support.bioconductor.org/p/p134163/
You are likely to get a better reply to this on bioconductor.
Your design matrix will depend on what questions you are trying to answer and the presence of confounders in those comparisons. Using all of your factor levels, can you describe some questions you want answered?