<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>

CC BY-SA 4.0
2020-06-05T07:19:10.990Z
thanks a lot Peter
beginner
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2020-06-04T20:42:16.483Z
2020-06-04T20:42:16.483Z
Peter Langfelder
<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>

<r><rna-seq><bioconductor><gene-expression><wgcna>
WGCNA co-expression network analysis with less than 20 samples
# 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 Peter  

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