DESEQ2 FORMULAS FOR PAIRED SAMPLES

Question

[Valentin]

Dear community, I really need some help regarding a rna-seq analysis I'm currently working on. We performed an experiment with about 40 samples/patients, cells stimulated vs control medium. Nothing hard here, just paired the samples with a "~ sample + condition" design.

However a new question now emerged and we're curious to know if other values influence the response to the stimuli (or "condition"). Let's say glycemia. If the samples weren't paired, then I believe the formula should've been "~ condition + glycemia + condition:glycemia", however this doesn't work if I try to add in the "sample" part to pair them up.

My questions are:

1. What would be the appropriate formula in this case?
2. What's the best approach for a numeric value in this case? Do I just scale it or cut it into factors?

Answer 1

[i.sudbery]

This is what the edgeR manual reffers to as a "within and between" design. Setting up the design matrix for such an expriment is non-trival, but possible. Although the steps in the edgeR manual are for edgeR, I think they shuold apply just as well to DESeq.