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nolanlab / cytospade

Cytoscape plugin for SPADE
http://cytospade.org
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CytoSPADE Plugin Issues #12

Open fkollingiv opened 10 years ago

fkollingiv commented 10 years ago

Hi All,

I have recently installed the spade R package and have had some early success in working through the pipeline with my own data. However, in an effort to make the package more accessible to the rest of my lab, I'm trying to move to the Cytoscape plugin rather than the R interface, but I'm unfortunately facing some issues:

When installing the plugin from R, everything seems to go smoothly and I get the expected "plugin has installed correctly" message.

In Cytoscape, I'm able to open the plugin, select files, choose markers for clustering and enter values for the sampling parameters.

My issue is that once at the "run" screen, pressing either Generate run spade script, or run Spade does nothing at all. In my working directory, the runSPADE.R script is generated but it is completely empty.

I am have tried this is both Cytoscape 2.8.2 and 2.8.3 with the same issue. I'm running R version 3.0.1 on 64bit Windows 7. I have also made sure to run R and Cytoscape as administrator to avoid weird permission issues.

Any help would be greatly appreciated!!

Fred

zbjornson commented 10 years ago

Hi Fred,

Unfortunately this is a known issue (see more discussion in a few issues under nolanlab/spade). It's on my to-do list to fix this, but is a low priority because Cytobank has a better UI for SPADE now.

fkollingiv commented 10 years ago

Hi Zach, Thanks for your help. I didn't see the other threads discussing this issue but it's good to know I'm not the only one. I will plan on moving over to Cytobank instead.

Best,

Fred

On Mon, Mar 10, 2014 at 3:04 PM, Zach Bjornson notifications@github.comwrote:

Hi Fred,

Unfortunately this is a known issue (see more discussion in a few issues under nolanlab/spade). It's on my to-do list to fix this, but is a low priority because Cytobank has a better UI for SPADE now.

Reply to this email directly or view it on GitHubhttps://github.com/nolanlab/cytospade/issues/12#issuecomment-37221155 .

Fred Kolling IV Graduate Student University of Connecticut Department of Molecular and Cell Biology

fkollingiv commented 10 years ago

Hi Zach,

Is the cytobank version of SPADE live yet? I've been stumbling through their interface and posts and haven't been able to find it. If not, is there an ETA?

Thanks!

zbjornson commented 10 years ago

Hi Fred, Yes, but only on certain servers. You can get started at https://dvs.cytobank.org/cytobank/signup and/or send an e-mail to support@cytobank.org. Zach

sythiel commented 10 years ago

Hi Zach, was wondering if the problem with Cytoscape had been resolved. Is there any workaround to make it work without having to move to Cytobank? Rossella