DGE analysis with >3 treatements

[jfo]

Hello,

I have 2 different phenotypes sampled in three populations, with three reps each. I performed the run_DE_analysis using per population and "global" (i.e. pool of phenotpye A in all pop vs pool of pheno B ).

However, when I did a Venn diagram, there were only a few genes common (<10) between the "global" and per treatment DGE (i.e. global vs pop1-phenoAxphenoB, etc.). My question is: Is it correct to compare the output of global and per pop analysis or should i just stick with the per pop analysis instead?

Thanks for the help!