Good morning all - I typically perform RNAseq DGE analysis using DESeq2, which forces you to set one group as "reference". The results obtained show differentially expressed genes for each group relative to reference
However, if instead I was interested in looking what genes uniquely marks each group, I could recombine groups (e.g. Group A vs B+C+D, B vs A+C+D, etc). This would be simple enough to do, and it seems to me like a fairly intuitive thing to do - kind of like "marker gene analysis" for clusters in single cell RNAseq. I just wonder why I haven't come across such a workflow performed by others (I realize it partially comes down to what the scientific question is).
Any thoughts as to whether this a scientifically/ statistically sound approach?