I am working on RNAseq dataset and now I performed the WGCNA using the expression data from deseq2. I wanted to create networks of two different conditions and wanted to compare them through network centralities. I have created the network using WGCNA and converted it into an igraph object but now when I am looking at the degree its shows the degree of all genes as 2.
I have a couple of quick questions 1) is my approach correct or i can not WGCNA generated networks not be compared this way?? 2) Have I done something wrong or missed something while creating WGCNA /coexpression networks?
Any help regarding this would be appreciated .
Thanks M W khan