Question: WGCNA cannot be done to compare two conditions?
gravatar for galiciaa
17 months ago by
galiciaa0 wrote:


I have been told I cannot use WGCNA with only two conditions (control and treatment). I am not sure why that would be the case and I would like to confirm if this is true? I have 3 samples for each condition so a total of 6 samples and I am not correlating to a quantifiable trait, I am only correlating the modules to the conditions.

Thank you

rna-seq wgcna • 806 views
ADD COMMENTlink modified 17 months ago by Ar1.0k • written 17 months ago by galiciaa0
gravatar for Ar
17 months ago by
United States
Ar1.0k wrote:

I believe it is not the condition but the number of replicates that are required for running WGCNA. Typically, you are required to have more than 15 samples. Ideally, I would recommend more than 30 replicates for each condition.

Here is the list of frequently asked questions:

Another advice would be plotting PCA/MDS plots to check if there are no Batch Effects or technical effects such as sex, non-biologicals effects.

Good luck!

ADD COMMENTlink written 17 months ago by Ar1.0k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1030 users visited in the last hour