Question: How to define and use samples of WGCNA
gravatar for afli
9 weeks ago by
China, Beijing, IGDB
afli140 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 • 129 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by afli140

can you show the code?what you are using ,

You have mostly technical replicates ..

ADD REPLYlink written 9 weeks ago by krushnach80440

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

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by afli140

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 9 weeks ago by Kevin Blighe33k

All right, thank you!

ADD REPLYlink written 9 weeks ago by afli140
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