I have a question regarding multiple samples in a paired dataset. I tried to conduct differential expression analysis between samples accessed from different sites of paired patients. For example, patient 1 may have a skin sample and two brain samples collected in this dataset.
Patient.ID Accession.Site 1 1 Skin 2 1 Skin 3 1 Brain 4 2 Brain 5 2 Brain 6 2 Skin
The design formula I used is
~ Patient.ID + Accession.Site
This may be trivial to ask but I want to have a clear idea whether DESeq2 model will average those multiple samples from the same site for the same patient.