Hi fellow DESeq'ers!

I am trying to figure out how to model a DEA with n paired samples (so n conditions + n controls, where the two sample sets come from the same individuals) plus two unrelated controls. So overall I am dealing with n condition + n+2 controls.

From the DESeq2 Vignette I could read that a paired experiment should be modeled as ~subject+condition, but I am wondering if this could work in my case as well.

Many many thanks in advance!

In DESeq2 which uses fixed effects, the unpaired samples do not contribute to more information about the condition effect, because they do not have a corresponding treatment sample. So you can leave them out.

There is another method in limma-voom, called duplicateCorrelation(), which allows you to include them, as it does some extra modeling on the degree of correlation between the paired samples.