text: user1369: 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?
  
  user851: It's hard to say without knowing how different the subtypes are. If you do a common WGCNA, you may find modules related to the differences between A and B as well as to drivers of expression variation in A and B (common and separate). Since A has fewer samples, the variation will have to be stronger to be reflected by WGCNA modules. 
  You can run the WGCNA, find modules that vary the most in A samples (these may or may not also vary in B samples), then see whether LncRNAs belong to these modules and have a high kME (module membership). 
  
original_text: 1369: <p>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). </p>
  
  <p>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.</p>
  
  <p>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?</p>
   851: <p>It's hard to say without knowing how different the subtypes are. If you do a common WGCNA, you may find modules related to the differences between A and B as well as to drivers of expression variation in A and B (common and separate). Since A has fewer samples, the variation will have to be stronger to be reflected by WGCNA modules. </p>
  
  <p>You can run the WGCNA, find modules that vary the most in A samples (these may or may not also vary in B samples), then see whether LncRNAs belong to these modules and have a high kME (module membership). </p>
  