Error with findModules() about pywgcna HOT 7 CLOSED

Hi,

it looks like you do have negative values, right?

also, preprocess() will run goodSamplesGenes(), why did you run it before you pass your matrix?

from pywgcna.

Hello, thank you for responding.

The goodSamplesGenes() was a oversight from an earlier test and has been removed.
What do you advise for the script? Is the negative values the cause?

from pywgcna.

it might be but I'm not sure ...
can you send me a subset of your data that will give you the same error?
you can change the row and column names of your data with something else if your data is not publicly available

from pywgcna.

data_heart_left_ventricle_sample.csv

Here is a subset of the dataset I am using, it is from https://gtexportal.org/home/datasets

from pywgcna.

I was able to run PyWGCNA on the dataset you provided!
I would suggest check the version of all your all the other packages which I listed mine here
also the python version I have is 3.10.4

I also put my script bellow just in case

import PyWGCNA
import pandas as pd

tpm = pd.read_csv('data_heart_left_ventricle_sample.csv', index_col=0)

test = PyWGCNA.WGCNA(name='GTEX-111FC',
                     species='Humans',
                     geneExp=tpm,
                     TOMType='unsigned',
                     powers=[10],
                     networkType="unsigned",
                     save=True)

test.preprocess()

test.findModules()

from pywgcna.

Thank you!
I reinstalled my packages with the same versions as the PyWGCNA requirements and everything runs as intended!
Before this issue is closed, are there any plans to add support for Cytoscape networks in future versions of PyWGCNA?
https://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html

from pywgcna.

great!

Sorry but for now, I don't have a plan to add support for Cytoscape networks:)
but if you want to give it a shot, you're welcome to do and I will be happy to help you integrate that with PyWGCNA

from pywgcna.