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nargesr avatar nargesr commented on July 26, 2024

Hi,

please try to install the last version of PyWGCNA and try to go through the tutorials again.

if you face the same error again, please send me your input, your code

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mgb217 avatar mgb217 commented on July 26, 2024

Hi,

please try to install the last version of PyWGCNA and try to go through the tutorials again.

if you face the same error again, please send me your input, your code

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mgb217 avatar mgb217 commented on July 26, 2024

Hi,

I change a compute node. There is no 'ValueError: Linkage 'Z' contains negative distances'. But I got another error:

import PyWGCNA
geneExp = '5xFAD_paper/expressionList.csv'
pyWGCNA_5xFAD = PyWGCNA.WGCNA(name='5xFAD',species='mus musculus',geneExpPath=geneExp,outputPath='',save=True)
Saving data to be True, checking requirements ...
Figure directory does not exist!
Creating figure directory!
pyWGCNA_5xFAD.preprocess()
Pre-processing...
Detecting genes and samples with too many missing values...
Done pre-processing..

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

[15 rows x 7 columns]
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!

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