How to select mergeCutHeight in WGCNA?
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harelarik ▴ 50
@harelarik-13564
Last seen 13 months ago
Israel

Hi,

 

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

 

 

 

Thank you,

 

Arik

 

WGCNA mergeCutHeight • 2.7k views
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@peter-langfelder-4469
Last seen 19 days 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

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