Question: How to define and use samples of WGCNA
gravatar for afli
2.3 years ago by
China, Beijing, IGDB
afli190 wrote:

Hi, in WGCNA manual I learn that the minimum sample size for WGCNA is 15. If I have 10 different treatment, each treatment has three replicates, do I have 30 samples or just 10 samples?

On the other hand, if I want to construct co-expression network of leaf tissue in drought condition, but the available RNA-seq samples of this are fewer than 15, would it be better to add RNA-seq data of leaf tissue in disease condition, salt stress condition and so on? or just keep and analyse the few samples? I wonder the gene regulation mode would maintain in different conditions, if not, add too many different RNA-seq samples may increase noise.

Thank you!


wgcna • 1.3k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by afli190

can you show the code?what you are using ,

You have mostly technical replicates ..

ADD REPLYlink written 2.3 years ago by krushnach80870

you mean three technical replicates is one sample, three biological replicates are three samples?

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by afli190

The value of 15 seems arbitrary to me - I am not sure that it is a hard threshold. If the developer of WGCNA went by the Aztec system of numbers, maybe he would have said that 20 is the minimum (Aztecs had 20-base system of numbers).

I would say that you have 30 samples.

ADD REPLYlink written 2.3 years ago by Kevin Blighe69k

All right, thank you!

ADD REPLYlink written 2.3 years ago by afli190
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