Hello everyone ，I want to known how to evaluate the quality of the module obtained from the WGCNA analysis. I analyzed about 3,000 genes with WGCNA and only got two modules. Does this have anything to do with the experimental grouping (only the control and experimental groups, there is no other information). In this case, how can I get my hubgenes. I'm looking forward to some advice. Thanks!
I will just focus on the main question, i.e., the identification of hub genes: if you just search in a search engine, you will easily find the solution. Thus, the easiest way is to simply use the chooseTopHubInEachModule function from WGCNA...
Take a look at this linked answer: A: How to find the hub genes in the gene co-expression network constructed by WGCNA