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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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Error appearance in PyWGCNA (version 1.2.4) in Google colaboratory #46

Open YoshifumiMiyagi opened 1 year ago

YoshifumiMiyagi commented 1 year ago

I ran PyWGCNA under Google colaboratory environment.

①　pyWGCNA_CC.findModules() →UnboundLocalError: local variable 'merge' referenced before assignment

②　pyWGCNA_CC.analyseWGCNA() →ValueError: 'box_aspect' and 'fig_aspect' must be positive

Details are below. PyWGCNA problem

We welcome your valuable input. Thank you in advance.

nargesr commented 1 year ago

Hi, as you see in your pip installation, there is an Error regarding your numpy version.

Please try to install numpy below 1.25. The one that I have is numpy==1.24.3.

YoshifumiMiyagi commented 1 year ago

Thank you for your input. The dependency issue arose and I was able to install the library with PyWGCNA 1.2.3 -> numpy update (1.24.3)-> PyWGCNA 1.2.4.

PyWGCNA problem 2

However, the error message remains in the analysis. I will consider trying in the Local environment, but I think it would improve the usability if I could analyze it in Google colab as well.

nargesr commented 1 year ago

I'm going to run it on Google Collab and will update you

li1553770945 commented 1 year ago

I used python==3.11,numpy==1.24.3,PyWGCNA==1.2.4 on my windows10 computer, and I also have this problem. Hopefully the author will fix it.

NegarMirgati commented 4 months ago

Hi, I've encountered this problem as well. We would greatly appreciate it if you could fix this problem. This might help.

nargesr commented 4 months ago

Hi @NegarMirgati,

would you mind telling me the version of PyWGCNA you used and the error you got?

also please tell me a little bit about your data. is it bulk? or something else?