Hello Everyone,

I'm trying to use WGCNA to analyze dose-response RNA-Seq data. I have 24 samples for 8 stimulation concentrations:

• Unstimulated (24 Samples)
• 640fM (24 Samples)
• 3.2pM (24 Samples)
• 16pM (24 Samples)
• 80pM (24 Samples)
• 400pM (24 Samples)
• 2nM (24 Samples)
• 10nM (24 Samples)

From what I've seen in the literature, samples from all conditions are usually inputted into one WGCNA analysis and the condition is then treated as a clinical trait which is later correlated with module eigengenes. However, I'm wondering if it's possible to generate a separate WGCNA analysis for each of the 8 conditions, then compare the results. For example, I'm using the same set of transcripts and the same beta value to run WGCNA once on the 24 Unstimulated samples and again on the 24 640fM samples; can I then confidently compare the two outputs in terms of connectivity metrics, the number of modules, gene significance, etc.?

Any advice is appreciated, thanks in advance.