how to evaluate the quality of modules analysisd from WGCNA

Question

[464406567]

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!

Answer 1

[Kevin Blighe]

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

Kevin

[464406567]

thanks for your advice! if there were just two modules obtained from WGCNA,can i continue to the next step to analysis the hubgene got from these two modules? In addition ,I am very confused that what is the reason why i just got two modules from the WGCNA analysis?

Tina

[Kevin Blighe]

With no information provided about your data, I cannot make any further comment in that regard. WGCNA is not highly regarded, by the way (does not have a good reputation). Results from WGCNA are highly variable and the interpretation of these [results] is always speculative. Were you asked to use WGCNA? What was your input data? What was the distribution of your input data? Which soft threshold did you choose, and why?