error while data loading in CoNet

[Khemlal Nirmalkar‏]

Hello Cytoscape users,

           I am using first time CoNet and Cytoscape. I tried with sample files and it ran successfully but when I tried with my files, shown some errors which is in below. Can someone help me what could be the possible mistake in my files.
 

Thanks,
Sincerely,
Khemlal

Error message:
java.lang.IllegalArgumentException: After filtering, less than 2 rows remain in the input matrix!
   
at be.ac.vub.bsb.cooccurrence.conversion.MatrixFilterer.filter(MatrixFilterer.java:373)
   
at be.ac.vub.bsb.cooccurrence.conversion.Preprocessor.processMatrix(Preprocessor.java:211)
   
at be.ac.vub.bsb.cooccurrence.conversion.Preprocessor.preprocess(Preprocessor.java:436)
   
at be.ac.vub.bsb.cooccurrence.cmd.CooccurrenceAnalyser.analyse(CooccurrenceAnalyser.java:3446)
   
at be.ac.vub.bsb.cytoscape.core.InferenceWorker.doInBackground(InferenceWorker.java:188)
   
at be.ac.vub.bsb.cytoscape.core.InferenceWorker.doInBackground(InferenceWorker.java:1)
   
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
   
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
   
at javax.swing.SwingWorker.run(SwingWorker.java:334)
   
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
   
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
   
at java.lang.Thread.run(Thread.java:748)


CoNet settings:
# CoNet vs. 1.1.1.beta compiled for Cytoscape 3.X parameter values
# Time of export: Tue Jun 05 21:20:40 CDT 2018
randroutine==edgeScores
randscorefile==/home/khemlal/Downloads/conet2017/conetNewBootstraps.txt
matrixtype==abundance
stand==col_norm
thresholdguessing==edgeNumber
guessingparam==1000.0

[piet molenaar‏]

Hi, 

this is apparently an error specific for the CoNet app, I'm cc-ing one of the authors,

Regards,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

[faustk...@gmail.com‏]

Dear Khemlal

Please check out the CoNet FAQ: http://psbweb05.psb.ugent.be/conet/faq.php

The relevant entry is: http://psbweb05.psb.ugent.be/conet/faq.php#tworows

Kind regards,

Karoline

[Khemlal Nirmalkar‏]

Hi Karoline,

           Thanks for your suggestion.

But I am sorry, I could not understand properly what is the meaning of this error message.

 in FAQ

Please can you explain me little bit more.

Here I attached my file (text file from biom, generated by qiime1 using silva104 database), if you have time can you look at once and tell me what is the mistake?

Sincerely,

Khemlal

Thanks,

Sincerely,

Khemlal Nirmalkar

(M.Sc. Microbiology)

Doctorate student

Department of Pharmacology

CINVESTAV-IPN, Zacatenco

México City, México

Email ID: Nirm...@cinvestav.mx

khemlaln...@gmail.com

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[najoua....@gmail.com‏]

Hello community,

I would like to know if this problem was solved ? I am encountring this issue using both the demonstration files and my own files.

My analysis was done using FROGS, the Biom file doesn't look like the one provided in the tutorial, so I am trying to run the analysis using an abundance table.

Any suggestions will be much appreciated.

Best,

Najoua

[Karoline Faust‏]

Dear Najoua

The error message ("After filtering, less than 2 rows remain in the input matrix!") means that after filtering rows (taxa) in your input matrix, not enough are left for building the network. You need to change the filter criteria, though it is not a good idea to build a network from taxa containing too many zeros.

Kind regards,

Karoline

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[Najoua MGHAZLI‏]

Dear Karoline,

Thank you so much for your reply, I will try to fix this issue as suggested.

Regards,

Najoua

On Wednesday, June 6, 2018 at 2:27:25 AM UTC, Khemlal Nirmalkar wrote: