Question: Minimum number of samples per treatment/group for WGCNA analysis
1
gravatar for Mau
5 months ago by
Mau20
Mau20 wrote:

Hi,

I am in the process of designing an RNA-seq experiment with a non-model organism. I would like to have 3 treatments/groups, and analyze my data with a gene coexpression network analysis like WGCNA.

Despite extensive searching, I am still dubious about how many samples I need. I know that I should aim for 15-20 samples total:

https://support.bioconductor.org/p/65124/ https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html

But those answers don't mention how many sample sizes are needed per treatment/group. For example, an experiment with 18 total samples and 2 treatments will have 9 samples per treatment, whereas if 6 treatments are used then there will only be 3 samples per treatment (assuming equal number of samples per treatment).

In my case, I think I will have 20-25 samples. I would prefer to use 3 treatments, but I rather limit my design to 2 treatments if my sample size is not big enough.

Thanks Mau

ADD COMMENTlink modified 5 months ago by agustin.gonvi10 • written 5 months ago by Mau20
Answer: Minimum number of samples per treatment/group for WGCNA analysis
1
gravatar for agustin.gonvi
5 months ago by
Cleveland, OH
agustin.gonvi10 wrote:

You need a recommended minimum of 15 samples to build a network using all samples together regardless of treatment. Intuitively I will say that if groups members are evenly distributed is better. On a second step, you will correlate modules with treatments and test for significance, the sample size on each group would depend on the effect size of your treatment. I don't remember reading any power study for this step. I will use as many samples as I can afford.

ADD COMMENTlink written 5 months ago by agustin.gonvi10
1

Thank you for your answer agustin.gonvi. In an experiment with 15 samples and 2 groups, each group will have 7-8 samples if they are evenly distributed, so I guess it would be OK to keep that sample size with three treatments, for a total of 21-24 samples.

ADD REPLYlink written 5 months ago by Mau20
Answer: Minimum number of samples per treatment/group for WGCNA analysis
0
gravatar for ravisaroch
5 months ago by
ravisaroch0
ravisaroch0 wrote:

Minimum 15-15 samples are required in both the cases (treatment as well as in control).

ADD COMMENTlink written 5 months ago by ravisaroch0

Thank you for your input ravisaroch, but could you elaborate a bit? The links I posted say that you need 15 samples total (treatment + control), and I an interested in an experimental design with more than two groups. Thanks

ADD REPLYlink written 5 months ago by Mau20
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