This is a theoretical question. I am trying to do a comparative analysis (meta-analysis, preservation analysis, differential analysis, etc.) on the mRNA expression network constructed from WGCNA. I acknowledge that we were advised to choose the least power during the "pick soft threshold" step. However, essentially, the networks I am trying to compare were using different power.
My question is: What would be an appropriate procedure to compare multiple networks?
- Does it matter if the networks are transformed by different power during the soft thresholding step?
- Similarly, does it matter if the networks/ modules were defined with different "deep" during the cut tree step?
I really appreciate your help.