Question: How to define and use samples of WGCNA
0
gravatar for afli
15 months ago by
afli190
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!

Aifu.

wgcna • 632 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by afli190

can you show the code?what you are using ,

You have mostly technical replicates ..

ADD REPLYlink written 15 months ago by krushnach80630

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

ADD REPLYlink modified 15 months ago • written 15 months ago by afli190
2

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 15 months ago by Kevin Blighe53k

All right, thank you!

ADD REPLYlink written 15 months ago by afli190
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