analyze network problem

[Simone Nardin Weis]

Hi, i don't know why I'm trying to do the Network Analysis but it doens't work. Only NeighborhoodConnectivity is calculated.

I created the network with pp interaction and a table file with max fold change.

Simone

[Scooter Morris]

Hi Simone,

    I'm assuming you are using Tools->NetworkAnalyzer->Network Analysis.  If so, you should see a number of new columns in your Node Table, and several Network Statistics in the Results Panel.  If you don't see anything else, there may be a problem with the network -- can you send us a session file?  Note that the built-in NetworkAnalyzer only looks at network topology, so your fold change information won't be taken into account.

-- scooter

[Simone Nardin Weis]

Hi Scooter,

Yes, the new columns are created, but all blank.

Do you have an e-mail to send you the session file. I would appreciate if you could help me.

Simone

[Simone Nardin Weis]

Scooter?

On Thursday, October 25, 2018 at 12:21:44 PM UTC-3, Simone Nardin Weis wrote:

Hi Scooter,

Yes, the new columns are created, but all blank.

Do you have an e-mail to send you the session file? I would appreciate if you could help me.

[Alex Pico]

I’ll follow up with you…

 - Alex

-- 
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/eebf8dda-f69f-47d5-8f6c-b6949cd160a5%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Simone Nardin Weis]

Hi Alex,

How can I do the network analysis in this session file? I tried but it returns all blank new columns.

Simone

On Thursday, October 25, 2018 at 6:23:15 PM UTC-3, Alex Pico wrote:

I’ll follow up with you…

 - Alex

018, at 1:05 PM, Simone Nardin Weis <sinard...@gmail.com> wrote:

Scooter?

On Thursday, October 25, 2018 at 12:21:44 PM UTC-3, Simone Nardin Weis wrote:

Hi Scooter,

Yes, the new columns are created, but all blank.

Do you have an e-mail to send you the session file? I would appreciate if you could help me.

Simone

On Thursday, October 25, 2018 at 12:09:56 PM UTC-3, Scooter Morris wrote:

Hi Simone,

    I'm assuming you are using Tools->NetworkAnalyzer->Network Analysis.  If so, you should see a number of new columns in your Node Table, and several Network Statistics in the Results Panel.  If you don't see anything else, there may be a problem with the network -- can you send us a session file?  Note that the built-in NetworkAnalyzer only looks at network topology, so your fold change information won't be taken into account.

-- scooter

On Thursday, October 25, 2018 at 7:57:02 AM UTC-7, Simone Nardin Weis wrote:

Hi, i don't know why I'm trying to do the Network Analysis but it doens't work. Only NeighborhoodConnectivity is calculated.

I created the network with pp interaction and a table file with max fold change.

Simone

-- 
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

[Alex Pico]

Hi Simone,

It just worked for me. Here’s what I did:

I cloned your network and removed all the empty columns (see “test1”). Then I chose: Tools > Network Analyzer > Network Analysis > Analyze Network… Then I chose “undirected”. Then all the columns were created and values were filled in (see “test 2”).

Can you open “test1” and try again?

If it still doesn’t work for you, at least you can use “test2”.  If you need to run this on other networks, I would try deleting the “Cytoscape Configuration” dir in your user directory and reinstalling Cytoscape. 

 - Alex

[Simone Nardin Weis]

Many thanks Alex!

Test1 doesn't work, test2 is fine! Thanks.

I'll reinstall cytoscape.

Simone