Question: WGCNA cannot be done to compare two conditions?
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gravatar for galiciaa
3 days ago by
galiciaa0
galiciaa0 wrote:

Hello,

I have been told I cannot use WGCNA with only two conditions (control and treatment). I am not sure why that would be the case and I would like to confirm if this is true? I have 3 samples for each condition so a total of 6 samples and I am not correlating to a quantifiable trait, I am only correlating the modules to the conditions.

Thank you

rna-seq wgcna • 48 views
ADD COMMENTlink modified 3 days ago by Ar860 • written 3 days ago by galiciaa0
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gravatar for Ar
3 days ago by
Ar860
United States
Ar860 wrote:

I believe it is not the condition but the number of replicates that are required for running WGCNA. Typically, you are required to have more than 15 samples. Ideally, I would recommend more than 30 replicates for each condition.

Here is the list of frequently asked questions: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html

Another advice would be plotting PCA/MDS plots to check if there are no Batch Effects or technical effects such as sex, non-biologicals effects.

Good luck!

ADD COMMENTlink written 3 days ago by Ar860
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