Unable to select nodes by id list file

[Michelle Toups]

I would like to select all genes within a certain node attribute category (i.e. disease). Some genes may belong to more than one disease. When I import my data, these common genes create a new category together (If it is listed as both disease 1 and 2 then the category becomes blank because cytoscape doesn't know where to place it). I thought I would upload each disease gene list, group each disease separately, then use a venn diagram plug in to illustrate the common ones (or something like this just for starting out). When I do this, the newest disease list over-rides the older one for all the common genes.

I attempted another way (selecting nodes by id list file) and ran into a second problem. 

I have read that cytoscape doesn't recognize .txt files so I used an excel with the simple format of:

node 1

node 2

node 3

..

Unfortunately, when I select by id list file, nothing happens. 

There must be a way (since multiple plugins exist to illustrate such a thing) to select nodes for each disease, despite some genes being common between the two diseases. 

The main question: Why won't cytoscape select nodes by id list file? I even triple checked that the node names were exactly the same and that all the same nodes and only the same nodes were found in the network. I created a fake file with only 3 nodes to see if these were selected. I searched all 3 gene names individually and it was selected correctly using the search bar but the id list file did not work. I also tried with a id list file that contains all the genes for the disease in the network and only those names (no extras that were not in the network). But nothing seems to be successful. 

[piet molenaar]

Hi Michelle,

This should work, can you send me your sample files so I can check what's wrong?

Cheers, Piet

--
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 http://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

--

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

[Michelle Toups]

Well, nothing happens when I use the sample data either. I used the galFiltered.sif and galFiltered.nodeAttrTable and then the id list file I used was just galExpData.xls. I think there is a step I am missing. I browse for and click my id list file and then nothing happens. Is there something I need to do after that to see the selection? 

[Michelle Toups]

(From the sample data)

Network  file:   galFiltered.sif

Attribute file:   galFiltered.nodeAttrTable

ID list     file:   Test.xlsx (my own file)

Check that these 4 nodes are found in the network by typing the names in the search bar. I found each of them. When I select nodes by ID list file, I expect to see 4 highlighted nodes but nothing happens. Please walk me through the steps utilizing these 3 files. Else, my file format may be wrong?

Thanks,

Michelle

On Thursday, July 30, 2015 at 2:11:19 PM UTC-4, Michelle Toups wrote:

Well, nothing happens when I use the sample data either. I used the galFiltered.sif and galFiltered.nodeAttrTable and then the id list file I used was just galExpData.xls. I think there is a step I am missing. I browse for and click my id list file and then nothing happens. Is there something I need to do after that to see the selection? 

On Thursday, July 30, 2015 at 12:17:55 PM UTC-4, Piet wrote:

Hi Michelle,

This should work, can you send me your sample files so I can check what's wrong?

Cheers, Piet

On Mon, Jul 27, 2015 at 3:57 PM, Michelle Toups <mto...@gmail.com> wrote:

I would like to select all genes within a certain node attribute category (i.e. disease). Some genes may belong to more than one disease. When I import my data, these common genes create a new category together (If it is listed as both disease 1 and 2 then the category becomes blank because cytoscape doesn't know where to place it). I thought I would upload each disease gene list, group each disease separately, then use a venn diagram plug in to illustrate the common ones (or something like this just for starting out). When I do this, the newest disease list over-rides the older one for all the common genes.

I attempted another way (selecting nodes by id list file) and ran into a second problem. 

I have read that cytoscape doesn't recognize .txt files so I used an excel with the simple format of:

node 1

node 2

node 3

..

Unfortunately, when I select by id list file, nothing happens. 

There must be a way (since multiple plugins exist to illustrate such a thing) to select nodes for each disease, despite some genes being common between the two diseases. 

The main question: Why won't cytoscape select nodes by id list file? I even triple checked that the node names were exactly the same and that all the same nodes and only the same nodes were found in the network. I created a fake file with only 3 nodes to see if these were selected. I searched all 3 gene names individually and it was selected correctly using the search bar but the id list file did not work. I also tried with a id list file that contains all the genes for the disease in the network and only those names (no extras that were not in the network). But nothing seems to be successful. 

--
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.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[Michelle Toups]

Thank you for your help. I was able to select by id list file when using the txt! 

[Julia Romanowska]

Hi,
I am having the same problem - what was the solution to yours?

[yuewu...@gmail.com]

I have similar problem, unable to select node using a text file each line as one node. What's you solution?

[Alex Pico]

Tips that have solved this issue so far:
 * Using a txt file (not xls)
 * Checking if some of your name column is empty

If anyone else has problems using this feature after trying the suggestions above, please post your issue and example files.

 - Alex

[dmfau...@lbl.gov]

I can't select multiple nodes from a file either. I'm using a .txt file.

On Saturday, March 24, 2018 at 12:20:35 PM UTC-7, Alex Pico wrote:

Tips that have solved this issue so far:
 * Using a txt file (not xls)
 * Checking if some of your name column is empty

If anyone else has problems using this feature after trying the suggestions above, please post your issue and example files.

 - Alex

[Alex Pico]

Can you provide a sample file and set of steps you’ve tried? Hard to reproduce or offer suggestions without more details.

 - 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 view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/4038956d-92a3-43fc-be45-4ae764fca560%40googlegroups.com.