Hello, I have two healthy and cancer data sets and want to do WGCNA analysis. My goal is to detect the genes that are significant/different in these two data sets comparing to each other. My questions is should I follow the second part (II. Consensus analysis of female and male liver expression data) in this page: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/
Or the third tutorial also consider the traits in calculation? I didn't see anything related to traits identifying in Adjacency and TOM calculation. But gene significance calculation get the traits information. So I am confused how the traits information is been considered in analysis. I will be thankful if you advice me what is the best way to use WGCNA for two data sets analysis.