I am in the process of designing an RNA-seq experiment with a non-model organism. I would like to have 3 treatments/groups, and analyze my data with a gene coexpression network analysis like WGCNA.
Despite extensive searching, I am still dubious about how many samples I need. I know that I should aim for 15-20 samples total:
But those answers don't mention how many sample sizes are needed per treatment/group. For example, an experiment with 18 total samples and 2 treatments will have 9 samples per treatment, whereas if 6 treatments are used then there will only be 3 samples per treatment (assuming equal number of samples per treatment).
In my case, I think I will have 20-25 samples. I would prefer to use 3 treatments, but I rather limit my design to 2 treatments if my sample size is not big enough.