I am doing WGCNA on methylation data (EPIC) from human blood samples and I'm stuck when choosing the soft threshold. I already made WGCNA on RNA-seq data before and the step of choosing the soft threshold was easy, with a high SFT.R.sq and a low mean connectivity (0.9 and 48). I selected the 240 000 most variable beta-values, but my methylation dataset doesn't seem to follow a scale free topology (the SFT.R.square is <0.7 and the mean connectivity is equal to several thousands). I saw here and here that I should take a beta of 12 (I have 45 samples). However, before running blockwiseModules(), I would like to know if someone else met this type of difficulty and how do you managed it. Were your results relevant with your biological question ?
Thanks a lot in advance,