Hello everyone,

I have a question about the experimental design for paired samples in DESeq2. In a typical setup where cell lines are derived from the same patient and measured under treatment and control conditions, I define the design as ~ sample id + condition.

How does DESeq2 interpret the sample id term in this case? Is it treated like a batch effect to be corrected for, similar to how one might correct for library type or sequencing batch? I don't think so, but I can't see how the package distinguishes between these two types of information.

Thank you very much for your support!

Anna

It's the same. The analysis will be run with adjustment for the donor differences. Technically, that's the same as a batch, being an unwanted variation to correct for. It doesn't matter how you call it, can be patient, batch or lollipop, all DESeq2 sees are categorical values.