Question: WGCNA configured network of low scale-free topology fit
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gravatar for chrisclarkson100
2.9 years ago by
chrisclarkson10030 wrote:

 

I have visually assessed a number of networks configured by WGCNA. The one that I am most happy with however only has a scale-free topology fit of 0.6 R^2.

As follows:

enter image description here

My downstream analysis of this is to correlate external trait-info to this network: how sure can I be of any inferred correlations if my network is of such a low R^2 fit?

wgcna • 1.4k views
ADD COMMENTlink modified 2.9 years ago by Peter Langfelder2.1k • written 2.9 years ago by chrisclarkson10030
Answer: WGCNA configured network of low scale-free topology fit
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gravatar for Peter Langfelder
2.9 years ago by
United States
Peter Langfelder2.1k wrote:

The fit of R^2 is not indicative of how trustworthy correlations of module eigengenes with external traits will be. Regarding low R^2, point 6 (I can't get a good scale-free topology index no matter how high I set the soft-thresholding power.) of WGCNA FAQ has some discussion.

If you have made sure that there are no technical or uninteresting biological drivers of global differences, you have used a reasonable soft thresholding power, and the modules look like distinct branches on the dendrogram, the modules are likely pretty stable and correlations with traits are trustworthy, inasmuch as you trust your data.

ADD COMMENTlink written 2.9 years ago by Peter Langfelder2.1k
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