local variable 'merge' referenced before assignment about pywgcna HOT 7 CLOSED

Hi,

Could you give me more information about how you got this error?
for example which version of PyWGCNA did you run?
did you change any default parameters? if yes, which one?
What was your input?

from pywgcna.

Hey,

I encountered the same error. My PyWGCNA version is 1.16.8. Could it be due to the only 1 identified module in the network?
As input, I had the preprocessed sc expression as a pd.DataFrame with genes as columns and cells as rows
Code I run:

exp_mat = pd.read_csv(dataset_path, index_col=0, header=0)
network = PyWGCNA.WGCNA(name='coexpression', geneExp=exp_mat)
network.findModules()

Traceback (most recent call last):
  File "~/.local/lib/python3.10/site-packages/PyWGCNA/wgcna.py", line 337, in findModules
    self.MEs = merge['newMEs']
UnboundLocalError: local variable 'merge' referenced before assignment

from pywgcna.

Hi,

The latest version is 1.2.4. Please install that one. Also, check the exact version of all the other dependencies here.

If you got the same error please send me your pickle object.

from pywgcna.

Hey!
I tried with the latest version and got the same error. Here is the pickle object:
coexpression.p.tar.gz

from pywgcna.

Hi @marie-minaeva

I wasn't able to read your pickle file. please make sure that you can read it through PyWGCNA.readWGCNA() and resend it again

from pywgcna.

Hi @nargesr,
Here is the new object. I additionally gzipped since GitHub doesn't allow sending .p files. Thanks!
coexpression.p.gz

from pywgcna.

Hi,

This is because you ended up with having only one modules.
I'll add warning at the end to avoid this error in future and give you warning instead of that

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