Question: Minimum number of samples per treatment/group for WGCNA analysis
0
gravatar for Mau
18 days ago by
Mau0
Mau0 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 10 days ago by agustin.gonvi10 • written 18 days ago by Mau0
Answer: Minimum number of samples per treatment/group for WGCNA analysis
1
gravatar for agustin.gonvi
10 days 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 10 days ago by agustin.gonvi10

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 10 days ago by Mau0
Answer: Minimum number of samples per treatment/group for WGCNA analysis
0
gravatar for ravisaroch
18 days ago by
ravisaroch0
ravisaroch0 wrote:

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

ADD COMMENTlink written 18 days 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 17 days ago by Mau0
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