0
$\begingroup$

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?

$\endgroup$
3
$\begingroup$

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).

| improve this answer | |
$\endgroup$
  • $\begingroup$ thanks a lot Peter $\endgroup$ – beginner Jun 5 at 7:19

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.