Degree sorted circle layout - Problem

[sikor]

hi all!

I have a problem with creating degree attribute for my network. When I
run Degree Sorted Layout the attribute is not created.
I'm running Cytoscape 2.6.3 on Windows XP with the Java version
1.6.0_15.
I tried to do the same with oldest version of Cytoscape, but this
problem also occured.

What can I do to solve my problem?

Thanks,
sikor

[piet molenaar]

Hi Sikor,
I'm not sure what you mean exactly.
Doesn't the layout work properly?
Or is the degree attribute not visible?
In my versions of Cytoscape it worked properly.
Piet

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Piet Molenaar
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Department of Human Genetics, M1-131
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[Cheng Luo]

I Just installed cytoscape 2.6.3 minutes ago. I saw that gene symbols
are likely very much different?
Actually I could have a lot of naive questions.

When I try to type in certain gene (human) and try to see the pathway,
for instance COX-2, then I see something like q8nf87, rsmn, etc., what
these symbiols are? no any ideas, how?
How to start from illumina gene expression microarray data? Cytoscape
read 35MB data?

Someone could help?

Thanks you very much!

Cheng

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[Peng-Liang Wang]

Sometimes, Degree attribute become invisible after running of other plugin. I did a fix, which will be available for Cytoscape 2.7. You can download AutomaticLayout.jar at http://chianti.ucsd.edu/svn/cytoscape/trunk/plugins/core/ and replace the one in the plugins directory of your Cytoscape install. Any problem, please let me know.

 

Peng