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mortazavilab / PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad415/7218311
MIT License
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Different results generated by v1.15 and v1.20 #74

Closed hanbinlu closed 6 months ago

hanbinlu commented 8 months ago

Hi,

Thank you for creating and maintaining this great package.

I recently upgraded pywgcna from 1.15.0 to 1.20.3, however, I got different results analyzing the same data. Version 1.15.0 resolved 50 modules and v1.20.3 67 modules. Do you have any insights on what factors causing the changes?

This is the code I ran:

wgcna_obj = PyWGCNA.WGCNA(
        name="rna_scaled",
        geneExp=geneExp,
        minModuleSize=50,
    )
wgcna_obj.findModules()

Thank you very much for your help, Hanbin

nargesr commented 8 months ago

Hi,

Thank you for your kind comments :)

there was a minor issue when I assigned modules to genes. it didn’t change stuff much in my test data so I didn’t think it should be making that huge changes.

One thing I would do is compare these PyWGCNA objects using Compare two PyWGCNA objects, so it will give you some insight into how the modules change