Since I've just started my analysis using WGCNA, I'm not really familiar with it so far. I need to do different comparisons in WGCNA. I have two ethnicities, for each of them I have three comparisons group, let's say A, B , C and among each of these, three classes (class1, class2, class3). For now, I run WGCNA for one ethnicity (all groups) - 8000 genes, after that I did gene set enrichment for each modules and I split my data set by groups while doing heatmaps for particular module. My other approach was to do WGCNA for a particular group (8000 genes). What I was thinking, if this is possible to take a list of 8000 most variable genes for each group A, B, C, then remove the genes that are the same for each group and run WGCNA on all of it. I'm using R, but I'm not sure how I should do that and which of these methods makes most sense.
Also, my question is, should I run DESeq2 on my data set before doing WGCNA? Thanks for help
