I have 10 different biological conditions and I would like to identify modules(gene sets) which are differentially regulated with respect to biological conditions. To do so,
I have calculated the fold chage for each of the conditions. Based on differential data , I have calculated gene to gene correlation (signed correlation) using wgcna and the modules have been identified. From dendrogram and heatmap, I can infer the module-module & module to trait relationship.
But, in wgcna tutorials, they have used preprocessed gene expression data (not differential data) for identifying the modules, and not differntial data. So,I would like to know that the procedure implemented ie., using differntial data to identify modules, is correct or not.
Thanking you for your time