DyNet input network ERROR

[jodas...@gmail.com]

Hello, I've run into a problem with the DyNet app for Cytoscape (I'm using version 3.7).

I created 2 gene networks with the GeneMania on Cytoscape app and I would like to compare them with DyNet, but when I input them to the DyNet analyzer I get this error:

use createListcolumn() to create List columns instead of createColumn for column '<name of the network>'.

Does anyone know why this happens?

What is the best way to produce networks to give DyNet as input? (I need to make my networks from lists of gene names).

Thank you in advance.

[Alex Pico]

Cc’ing the author of the app to help out…

http://apps.cytoscape.org/apps/dynet

 - Alex

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[David Lynn]

Thanks Alex for forwarding this message.

 

Jodasenju90 (sorry no name is given in the message below) – can you please send me the 2 networks you are trying to compare using DyNet and we will try see what the issue is.

Please also provide as much information as possible as to how you imported the networks into DyNet and what steps you took to generate the error.

Some screenshots might also help.

 

Kind regards,

David.

 

David J. Lynn
Director, Computational & Systems Biology Program. Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia.

Group Leader, SAHMRI Microbiome & Host Health Program.

EMBL Australia Group Leader.

Professor, College of Medicine & Public Health, Flinders University.

P +61 881 284 053
M +61 400 014 429
E david...@sahmri.com

PO Box 11060, Adelaide SA 5001, Australia.

www.sahmri.com

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[Giovanni Spirito]

Hello, thank you very much for the response.

The rationale of the analysis is that I have 2 lists of genes (only gene names), one list of genes liked to a disease and one list of candidate genes which I want to know whether they could be linked to the disease.

I downloaded Cytoscape 3.7, the GeneMania app and the DyNet app.

1. First I created two networks with the GeneMania app in Cytoscape, by pasting the gene lists in the search bar:

2. Then I went apps > DyNet analyzer, and selected the two networks I created:

3. When I click 'ok' I get this error:

I also tried to make networks with other tools such as STRING, but I get the same error.

The process works fine with the networks provided in https://bitbucket.org/dynetteam/dynet (EGFR_Inferred_Dyanmic_Tissue_Interaction_Network).

So I guessed it's a format issue, but I'm not able to piece together how to make a network I can give DyNet as input (it's the first time I work with any kind of network).

Thank you for the support,

Giovanni

Il giorno venerdì 6 settembre 2019 01:47:03 UTC+2, David Lynn ha scritto:

Thanks Alex for forwarding this message.

 

Jodasenju90 (sorry no name is given in the message below) – can you please send me the 2 networks you are trying to compare using DyNet and we will try see what the issue is.

Please also provide as much information as possible as to how you imported the networks into DyNet and what steps you took to generate the error.

Some screenshots might also help.

 

Kind regards,

David.

 

David J. Lynn
Director, Computational & Systems Biology Program. Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia.

Group Leader, SAHMRI Microbiome & Host Health Program.

EMBL Australia Group Leader.

Professor, College of Medicine & Public Health, Flinders University.

P +61 881 284 053
M +61 400 014 429

E davi...@sahmri.com

PO Box 11060, Adelaide SA 5001, Australia.

www.sahmri.com

Follow us on Facebook and Twitter.

This e-mail (including any attachments) is for the use of the intended recipient(s) only and may contain information which is confidential, privileged and/or subject to copyright. If you have received this e-mail in error, please notify the sender immediately and then delete the email and any attachments. If you are not the intended recipient, you must not use, disclose or distribute this e-mail or any attachment. We have taken precautions to minimise the risk of transmitting software viruses, but we advise you to carry out your own virus checks on any attachment to this e-mail. We do not accept liability for any loss or damage caused by software viruses.

 

From: Alex Pico <alex...@gladstone.ucsf.edu>
Sent: Friday, 6 September 2019 6:35 AM
To: cytoscape...@googlegroups.com
Cc: David Lynn <Davi...@sahmri.com>
Subject: Re: [cytoscape-helpdesk] DyNet input network ERROR

 

Cc’ing the author of the app to help out…

http://apps.cytoscape.org/apps/dynet

 

 - Alex

 

 

On Sep 5, 2019, at 6:26 AM, jodas...@gmail.com wrote:

 

 

Hello, I've run into a problem with the DyNet app for Cytoscape (I'm using version 3.7).

 

I created 2 gene networks with the GeneMania on Cytoscape app and I would like to compare them with DyNet, but when I input them to the DyNet analyzer I get this error:

 

use createListcolumn() to create List columns instead of createColumn for column '<name of the network>'.

Does anyone know why this happens?

What is the best way to produce networks to give DyNet as input? (I need to make my networks from lists of gene names).

 

Thank you in advance.

 

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[Giovanni Spirito]

Hello, thanks for the reply. I had already tried to export and re-import the networks, but that resulted in the same error. I also tried with bigger networks. I attach the two networks.

Thanks,

Giovanni