WGCNA Soft Threshold Target for RNASeq Data

Question

[Tyler.Akonom]

Hi all! I'm currently working through a WGCNA with an RNASeq data set. I've been having a hard time finding out what sort of soft threshold power I should be looking for compared to the tutorial in step 2a. The tutorial says to set an "h" value of 0.9, but none of my samples end up with that high of an R^2 value. Is there a reason to ever dip below that seemingly magic number of .9? Thanks!

Answer 1

[Kevin Blighe]

You can choose any value. Can you please explain more about your data, i.e., how it was processed?