WGCNA mean connectivity

Question

[jms2520]

I am wondering if someone can explain to me a good benchmark for mean connectivity in WGCNA. I have searched for other posts that may explain this but I can't get a good handle on how high "too high" is for mean connectivity. Is there such a thing?

Answer 1

[andres.firrincieli]

From the FAQ:

If the scale-free topology fit index fails to reach values above 0.8 for reasonable powers (less than 15 for unsigned or signed hybrid networks, and less than 30 for signed networks) and the mean connectivity remains relatively high (in the hundreds or above), chances are that the data exhibit a strong driver that makes a subset of the samples globally different from the rest. The difference causes high correlation among large groups of genes which invalidates the assumption of the scale-free topology approximation.

Always from the FAQ

If the lack of scale-free topology fit turns out to be caused by an interesting biological variable that one does not want to remove (i.e., adjust the data for), the appropriate soft-thresholding power can be chosen based on the number of samples as in the table below. This table has been updated in December 2017 to make the resulting networks conservative.

Number of samples   Unsigned and signed hybrid networks Signed networks
Less than 20                              9                       18
20-30                                     8                       16
30-40                                     7                       14
more than 40                              6                       12