Answers.Body: <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>
  
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Answers.CreationDate: 2020-06-05T07:19:10.990Z
Answers.Text: thanks a lot Peter
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Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-04T20:42:16.483Z
Answers.LastActivityDate: 2020-06-04T20:42:16.483Z
Answers.UserDisplayName: Peter Langfelder
Body: <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>
  
Tags: <r><rna-seq><bioconductor><gene-expression><wgcna>
Title: WGCNA co-expression network analysis with less than 20 samples
ThreadText: # WGCNA co-expression network analysis with less than 20 samples
  
  (Asked by: username_0 on 2020-06-04)
  
  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?
  
  **Tags:** r, rna-seq, bioconductor, gene-expression, wgcna
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2020-06-04. Score: 3 | Accepted answer
  
  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).
  
  > **Comments:**
  > **username_0**: thanks a lot username_1  
  
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