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?

1. Does it matter if the networks are transformed by different power during the soft thresholding step?
2. Similarly, does it matter if the networks/ modules were defined with different "deep" during the cut tree step?

I really appreciate your help.

Your question is off-topic for this site. WGCNA is not a Bioconductor package, and this site is meant to help people with technical questions about Bioconductor packages (your question is not technical, but statistical/theoretical). You should use biostars.org for this sort of question.