pyWGCNA.findModules()—— sys.exit("Error!") about pywgcna HOT 9 CLOSED

Hi,

Can you share with me your pickle file or a subset of your data that gave you this error?

from pywgcna.

Hi，
This is the data link: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44183/suppl/GSE44183_human_expression_mat.txt.gz

thank you

from pywgcna.

Hi, I had the same problem when I tried to replicate the example in quick start.

The session info was:

session_info.show()

PyWGCNA NA
session_info 1.0.0

Python 3.9.16 (main, May 17 2023, 23:02:07) [GCC 10.2.0]
Linux-4.9.0-6-amd64-x86_64-with-glibc2.24

Session information updated at 2023-05-18 13:00

The error was:

pyWGCNA_5xFAD.findModules()
Run WGCNA...
pickSoftThreshold: calculating connectivity for given powers...
will use block size 1876
Power SFT.R.sq slope truncated R.sq mean(k) median(k) max(k)
0 1 0.368857 -0.481613 0.701585 2444.750756 2260.416614 5665.102661
1 2 0.7253 -0.99165 0.886361 840.665489 673.081241 3009.058821
2 3 0.791986 -1.194264 0.946969 385.685335 258.451265 1916.810605
3 4 0.835392 -1.3419 0.968446 207.404152 113.456087 1332.762771
4 5 0.853842 -1.472183 0.973346 123.232581 54.784481 984.036824
5 6 0.870673 -1.553348 0.979584 78.455923 28.47124 752.959999
6 7 0.886736 -1.600869 0.986635 52.572016 15.594822 591.514192
7 8 0.896672 -1.639343 0.992373 36.65884 9.454046 475.817182
8 9 0.903531 -1.677747 0.994643 26.397061 6.024431 389.237531
9 10 0.906045 -1.706474 0.995895 19.521431 3.975959 322.823838
10 11 0.905582 -1.731076 0.994806 14.767291 2.623921 270.867416
11 13 0.914482 -1.751347 0.997466 8.941254 1.205108 196.222414
12 15 0.912684 -1.771227 0.994189 5.759987 0.568044 146.575349
13 17 0.912188 -1.774908 0.990829 3.905403 0.273242 112.189052
14 19 0.907649 -1.774186 0.989457 2.766824 0.135454 87.594344
Selected power to have scale free network is 9.
calculating adjacency matrix ...
Done..

calculating TOM similarity matrix ...
Done..

Going through the merge tree...
..cutHeight not given, setting it to 0.996 ===> 99% of the (truncated) height range in dendro.
Done..

Calculating 22 module eigengenes in given set...
..principal component calculation for module black failed with the following error:
..hub genes will be used instead of principal components.
Error!

from pywgcna.

Hi @ZivTQ,

I was able to run PyWGCNA on your data without getting any error. I would check if you have the latest version of PyWGCNA and maybe create new environment and install PyWGCNA from scratch.

Also make sure that you pass your data correctly, i.e you have to transpose your matrix
I attached my code to make sure you pass your input correctly:

import PyWGCNA
import pandas as pd

tpm = pd.read_csv('GSE44183_human_expression_mat.txt', sep='\t', index_col=0).T

test = PyWGCNA.WGCNA(name='test',
                     species='human', ## check this one 
                     geneExp=tpm, 
                     outputPath='',
                     save=True)

test.preprocess()
test.findModules()

from pywgcna.

Hi @jerviedog,

according to your session info, it seems you don't the latest version of the PyWGCNA

from pywgcna.

Hi @nargesr

Maybe you are right. But I just cloned the repo and installed PyWGCNA by python3.9 -m pip install .

Where can I find the latest version of PyWGCNA?

Thanks a lot.

from pywgcna.

Hi, @nargesr

I uninstalled PyWGCNA and reinstalled PyWGCNA by python3.9 -m pip install PyWGCNA==1.16.8

I still got the same error.

It is weird that the version of PyWGCNA is still 1.0.0 (shown by session_info.show()); but the pip freeze shows that the PyWGCNA version is 1.6.8.

from pywgcna.

Hi @jerviedog,

1.2.3 is the latest version, so hopefully installing that will solve your problem
but if you still get that error maybe it's good to check the version of other packages I used from here

from pywgcna.

Hi @ZivTQ,

I was able to run PyWGCNA on your data without getting any error. I would check if you have the latest version of PyWGCNA and maybe create new environment and install PyWGCNA from scratch.

Also make sure that you pass your data correctly, i.e you have to transpose your matrix I attached my code to make sure you pass your input correctly:

import PyWGCNA
import pandas as pd

tpm = pd.read_csv('GSE44183_human_expression_mat.txt', sep='\t', index_col=0).T

test = PyWGCNA.WGCNA(name='test',
                     species='human', ## check this one 
                     geneExp=tpm, 
                     outputPath='',
                     save=True)

test.preprocess()
test.findModules()

from pywgcna.