I construct my reference and validation network via WGCNA. In both network, I found similar modules in 2 network that one of them is green. Also, that is my prognostic module and I would like to find hub genes in the green module. My green module in Ref. Network has 948 genes and in validation network has 661. By intersect() function, I compare gene symbol in two modules but I found just 5 genes as common. My network type is “Signed” and the correlation method is “Pearson”. I don’t know why does it happen and which factors have effect in my study. That is important for me because I have found some hub genes in the green module in my ref. network and for validation that I need to find that hub genes into the green module in validation network. Generally, do I have another way for hub gene validation?
I appreciate if anybody share his/her comment with me.