Hi
Thanks for providing PyWGCNA.
I am running using my data. In the step pyWGCNA.findModules(), I got Error
Calculating 29 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.
An exception has occurred, use %tb to see the full traceback.
SystemExit: Error!
`SystemExit Traceback (most recent call last)
Input In [6], in <cell line: 1>()
----> 1 pyWGCNA.findModules()
File ~\AppData\Roaming\Python\Python39\site-packages\PyWGCNA\wgcna.py:300, in WGCNA.findModules(self, **kwargs)
297 self.datExpr.var['dynamicColors'] = WGCNA.labels2colors(labels=dynamicMods)
299 # Calculate eigengenes
--> 300 MEList = WGCNA.moduleEigengenes(expr=self.datExpr.to_df(), colors=self.datExpr.var['dynamicColors'])
302 self.MEs = MEList['eigengenes']
303 if 'MEgrey' in self.MEs.columns:
File ~\AppData\Roaming\Python\Python39\site-packages\PyWGCNA\wgcna.py:2036, in WGCNA.moduleEigengenes(expr, colors, impute, nPC, align, excludeGrey, grey, subHubs, softPower, scaleVar, trapErrors)
2034 if not check:
2035 if not trapErrors:
-> 2036 sys.exit("Error!")
2037 print(" ..ME calculation of module", modulename, "failed with the following error:", flush=True)
2038 print(" ", pc, " ..the offending module has been removed.", flush=True)
SystemExit: Error!`
The running log as following:
Run WGCNA...
pickSoftThreshold: calculating connectivity for given powers...
will use block size 3104
Power SFT.R.sq slope truncated R.sq mean(k) median(k)
0 1 0.019005 0.439419 0.944844 1583.917996 1554.807821
1 2 0.06366 -0.584601 0.929494 670.43699 652.433442
2 3 0.309456 -1.103302 0.942454 354.841864 335.688239
3 4 0.463625 -1.258173 0.934568 214.286872 195.668517
4 5 0.551524 -1.377 0.910081 141.322811 123.364176
5 6 0.665052 -1.332488 0.935139 99.308738 82.414462
6 7 0.808912 -1.275045 0.99298 73.223957 57.040702
7 8 0.861059 -1.346268 0.995675 56.071326 40.420707
8 9 0.899288 -1.39177 0.995843 44.268053 29.410026
9 10 0.915354 -1.439295 0.99548 35.840468 21.702019
10 11 0.930287 -1.462413 0.99669 29.635947 16.249537
11 13 0.94553 -1.491679 0.996215 21.327587 9.572117
12 15 0.95332 -1.479453 0.996157 16.193779 5.931626
13 17 0.954481 -1.464538 0.993863 12.811008 3.774937
14 19 0.953151 -1.434312 0.988609 10.466524 2.496161
0 2757.869438
1 1459.46165
2 910.290623
3 627.926617
4 477.597429
5 375.88095
6 308.184438
7 269.243033
8 238.667545
9 217.831659
10 200.730955
11 174.80621
12 156.010401
13 141.336406
14 129.549861
Selected power to have scale free network is 10.
calculating adjacency matrix ...
Done..
calculating TOM similarity matrix ...
Done..
Going through the merge tree...
..cutHeight not given, setting it to 0.994 ===> 99% of the (truncated) height range in dendro.
Done..
Calculating 29 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.
An exception has occurred, use %tb to see the full traceback.
SystemExit: Error!
thanks