I have two cancer subtypes data. Subtype A is 14 samples and Subtype B is 23 samples. I'm interested in identifying the functions of some LncRNAs in the Subtype A group. For this I'm using all protein-coding genes and interested LncRNAs expression data (normalised counts).
From the WGCNA tutorial, I see that minimum number of samples needs to be 20. So, I guess using only Subtype A 14 samples for the analysis is not possible.
Can I use both Subtype A 14 samples and Subtype B 23 samples together for the analysis? In case if I use both, once I get the modules how do I know that the genes in modules are related to Subtype A or Subtype B? The pathways I get from the interested module is related to Subtype a or Subtype B? How this can be identified?