Hello;

I have a questions regarding differential network analysis. I have created my two separate networks using wgcna. Since the networks are different (have different samples); they also have different soft threshold beta power to fit scale free. I saw that on previous studies; people kept the power the same for two networks as long as they fit scale free. However; I can't do that because these networks do not fit scale free at the same powers. Can I still compare the networks for different centrality measures based on their soft threshold power. I want to be sure that the difference in topology I am seeing is not because of the power but the underlying condition. Any inputs appreciated.

Thanks!

Cross-posted and answered: https://www.biostars.org/p/492043/

Kevin