Entering edit mode
Hi fellow DESeq'ers!
I have a dataset of 180 RNA-seq samples for which I run differential expression analysis using deseq2! I have a mixed up of paired samples and unpaired samples: 60 paired samples (30 cases vs 30 controls from 30 patients) and 120 samples unpaired from 120 patients either case and control! I am wondering if I can use the paired analysis offered by deseq2 in this case ? here is my fomrula
formula(~ sequenicng_lane + Patient_id + status)
Thanks in advance; Fatemeh
Thanks. I already saw this but there, the question is somehow different in my case most of the samples are unpaired and they are either case or control!