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cstoeckert / iterativeWGCNA

Extension of the WGCNA program to improve the eigengene similarity of modules and increase the overall number of genes in modules.
GNU General Public License v2.0
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Problems reading the input file #34

Closed jcabanad closed 3 years ago

jcabanad commented 3 years ago

Hi!

Thank you very much for such an amazing tool. I'm trying to use it for my data and I have problems reading the input file. I have a .txt file with one row per gene and one column per sample, as it is described in the code. It can read the file and detect properly the number of genes, however, when I run the software it say that there are 0 samples.

This is the command I'm using

python run_iterative_wgcna.py -i /home/juditc/ADHD/GWAS_TDAH/TDAH/WGCNA/iterativeWGCNA/data_WGCNA_micro/datExpr_trans.txt --wgcnaParameters maxBlockSize=20000,corType=bicor,power=4,minModuleSize=30,saveTOMs=FALSE,minKMEtoStay=0.8,minCoreKME=0.8,networkType=signed,numericLabels=TRUE -o /home/juditc/ADHD/GWAS_TDAH/TDAH/WGCNA/iterativeWGCNA/results_WGCNA_micr/ -v

this is how my expression file look like:

gene CNT0004 CNT0005 CNT0006 CNT0008 CNT0009 CNT0010 CNT0011 CNT0013 CNT0015 7896759 4.87840123385933 5.38352783819666 5.27055629800665 5.03304817148139 7896761 3.52810116520177 3.64393642429303 3.70436640713184 3.90670441357473 7896779 4.45185105685781 4.35454380046519 4.54187108060689 4.69967854721333

Best regards,

Judit

fossilfriend commented 3 years ago

Judit-

I am sorry to hear you are having issues reading your input file. Is your file tab- or space-delimited? Currently iterativeWGCNA only handles tab-delimited input.

-Emily

jcabanad commented 3 years ago

Hi Emily,

I have double checked the file and I had a problem with the separators as you suggested. Sorry for the incovenience.

Best,

Judit