How to select mergeCutHeight in WGCNA?
1
0
Entering edit mode
harelarik ▴ 60
@harelarik-13564
Last seen 3.0 years ago
Israel

Hi,

 

What is would be a good way to select mergeCutHeight for modules generation with  blockwiseModules?

 

 

 

Thank you,

 

Arik

 

WGCNA mergeCutHeight • 4.9k views
ADD COMMENT
2
Entering edit mode
@peter-langfelder-4469
Last seen 6 months ago
United States

I am not aware of a principle from which one could derive an "appropriate" value, but in practice, on data sets with 50-100 samples, using 0.15 to 0.2 has worked fairly well. For fewer samples a larger valuse (0.25 to 0.3) may be warranted. If you want larger modules, increase the value; if you want smaller modules at the risk of having redundant modules (modules with very similar functional annotation and very similar fuzzy module membership), you can decrease the value to say 0.10, maybe even lower if you have lots of samples (hundreds or more).

HTH

Peter

ADD COMMENT
0
Entering edit mode

Thank you!

ADD REPLY

Login before adding your answer.

Traffic: 306 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6