Error selecting species in stringApp on Cytoscape

Question

[Regan]

Hello!

I'm relatively new to using cytoscape and I am trying to generate networks from proteomics datasets. I have been following the protocols for omics visualizer and stringApp from Lars Juhl Jensen (). However, I'm having a problem with retrieving a string network. After uploading my data through omics visualizer, I click the string icon above the omics visualizer table and am given the options for species/protein ID column/confidence score. When I try to select the drop down for species it just flashes and nothing happens. If I try to retrieve a network, I'm given the error: "Unknown species 'null'".

I've tried reinstalling, different data sets, different files type, etc. so any advice on how to get around this would be appreciated!

-Regan

Answer 1

[xanderpico]

It's hard to say exactly what's going on. The app works in general for me and other reporting users. Here are some suggestions:

• Confirm that the STRING app is installed
• Try using the STRING app directly to retrieve a network. If that works, then try the Omics Viz tool again. If that does not work, then at least you have isolated the issue to the STRING step.

After try the above, you could then email the authors of the apps directly. Contact info is on every Cytoscape app store page. Both apps are actively developed and you should get a direct response.