Hi all, I am working on using WGCNA for a bulk RNA-seq experiment. I have three experimental conditions (control, treatment 1, and treatment 2) and have a total sample size of 18 (6 per group). Using the online WGCNA tutorials, I could analyze my datasets after variance stabilizing transformation (vst). I got the summary of network analysis results as a CSV with Gene significance (GS), p.GS, module membership(MM), and associated p-value (p.MM).
I want to extract a set of significant genes from the module with the highest positive correlation to my treatment conditions. As I am just getting acquainted with WGCNA interpretation, which of these parameters in the CSV should I use for filtering further (GS, p.GS, and module membership and associated p-value (p.MM))?
Also, how would I choose the limits of the criteria? Should it be using the scatter plot (MM vs GS)?
As I am pretty new to WGCNA, any help is appreciated. Thanks in advance!
for single-cell data, there is a GetModules function: https://divingintogeneticsandgenomics.com/post/how-to-do-gene-correlation-for-single-cell-rnaseq-data-part-2-using-meta-cell/ There should be a similar function for bulk data.