Question: Reactome Fi Plugin Cytoscape Help
1
gravatar for Tanvi
7.9 years ago by
Tanvi10
Tanvi10 wrote:

Reactome FI Plugin cytoscape help

I have microarray data and using reactome FI plugin in cytoscape I want to build gene interaction network.

After loading the expression data (1st column gene name and other columns samples with respective values) it is showing 0 modules in table as a result of MCL clustering with default parameters. And hence it is not giving the network output.

I dont know what is going wrong.

Thanks in advance !!

gene network cytoscape microarray • 2.7k views
ADD COMMENTlink modified 7.9 years ago by Robin Haw160 • written 7.9 years ago by Tanvi10

Which Cytoscape version are you using (should be 2.7.0 or above)

ADD REPLYlink written 7.9 years ago by Chris Evelo10.0k
2
gravatar for Robin Haw
7.8 years ago by
Robin Haw160
Toronto
Robin Haw160 wrote:

The Reactome FI plugin does not include example files when you download the jar fle. However, if you go to the Reactome FI plugin User Guide (also accessible from the Cytoscape plugins menu>Reactome FIs>User Guide), you will find a number of example files that can be used with the Reactome plugin.

If you have any further questions please contact me at the Reactome helpdesk (help@reactome.org).

Robin

ADD COMMENTlink written 7.8 years ago by Robin Haw160
0
gravatar for Tanvi
7.9 years ago by
Tanvi0
Tanvi0 wrote:

Version is 2.8. I have downloaded a few weeks ago. There is no example file provided by reactome FI plugin tutorial. Hence I am not getting if I am missing something in the input gene expression file.

ADD COMMENTlink written 7.9 years ago by Tanvi0

You could just have asked this information to your question (using edit). It is not an answer but more info about your question.

ADD REPLYlink written 7.9 years ago by Chris Evelo10.0k
0
gravatar for Chris Evelo
7.9 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

In that case I would e-mail the Reactome team and ask them to add an example data set to the tutorial. That will probably help more people and in my experience they are very helpful.

ADD COMMENTlink written 7.9 years ago by Chris Evelo10.0k
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