Comments (3)
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
from pywgcna.
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
from pywgcna.
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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Related Issues (20)
- how to set figsize HOT 2
- SystemExit: All your genes ended up in one modules! Reconsider your input parameters in order to get more modules. HOT 6
- Gene Significance HOT 1
- Correlation matrix HOT 6
- ask for some questions HOT 3
- Image too large. How suppress drawing when using pyWGCNA_obj.preprocess() ? HOT 3
- RecursionError when run pyWGCNA_ct.preprocess() HOT 1
- getDatTraits method might not be suitable for continuous traits. HOT 1
- How adjust parameter in functions??
- Genes and samples switched in goodSamplesGenes HOT 3
- error experienced in tutorial HOT 6
- Doubt on application HOT 1
- What other methods to define metadata colors are allowed, besides color labels ('black', 'pink', etc)? HOT 1
- Seeking help on `order` Parameter Usage and Metadata Color Settings HOT 13
- a issue for findModules() HOT 3
- findModules() inappropriately passes all kwargs to pickSoftThreshold() and cuttreeHybrid() HOT 2
- Re-naming modules HOT 1
- In the module Network Plot, Can we label the node as gene_name instead of gene_id ? HOT 2
- Several errors when performing findModules steps individually HOT 8
- 2
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