Hi, I am still trying to apply the consensus WGCNA to my own data following the Tutorial written by Peter Langfelder and Steve Horvath. I managed to draw the preservation heatmap etc, which corresponds to Figure 1 in the Tutorial II.5 (https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/Consensus-EigengeneNetworks.pdf). If I understood correctly the consensus modules are the preserved ones between both data sets.
But how do I obtain the differentially connected genes on my two data sets?
I also have a large number of consensus modules (=88), which makes these heatmaps a bit confusing. Do you have here any recommendations?
Thanks for your advices, Jutta