Query regarding WGCNA module formation
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4 months ago
abhisek061 ▴ 30

I want to form a WGCNA module, I took the genes which are expressed highly according to their standard deviation of my desired sample group, I want to ask is their need to normalize the gene count series matrix again before doing the experiment?

Please tell me there is a total of 9 samples and I choose highly expressed 4000 genes in 9 samples. What type of normalized procedure is needed?

WGCNA R RNA-seq • 206 views
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Entering edit mode
4 months ago

Don't bother using WGCNA if you have just 9 samples. WGCNA authors suggests > 20 samples, while 15 is the minimum number of samples (link)

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