WGCNA with low number of samples

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3.2 years ago

dahun73 ▴ 10

Hello All,

I'm studying further analysis of RNA-seq. I'm curious about which genes are connected and possible as target genes. So I started to use WGCNA. Actually, it is limited to run RNA-seq more than 20 samples by condition. So, I have just 2 biological replicates by condition. According to manual of WGCNA, it should be more than 15 samples. Despite this situation, how can I use WGCNA with small number of samples? Or, is there any good suggestion to use WGCNA? I appreciate any reply. Thank you in advance.

RNA-Seq WGCNA • 751 views

ADD COMMENT • link 3.2 years ago by dahun73 ▴ 10

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I am always surprised that people assume one can simply ignore the expert opinion of the developers. If you have < 15 samples you should not use the tool, it is not going to produce meaningful results with few samples. I'd accept that and find other ways to answer your biological question. Chasing ghosts based on noisy results from a tool that was not designed for the purpose you try to tweak it for is not helping I guess.

ADD REPLY • link 3.2 years ago by ATpoint 82k

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