Cytospade question/issue

[dbottomly]

I am using R-3.0.2 with spade version 1.10.2 and Cytoscape version 2.8.3 on Mac OSX 10.8.5. Both the R and Cytoscape plugin installation seemed to occur properly. I copied the bundled FCS file (SimulatedRawData.fcs) into its own directory and tried to using the Cytoscape plugin. I was able to select the containing directory and select the clustering markers. The 'Create Median and Fold Change Calculation' screen however does not allow anything to be done with that example (aside from saving the panel) and the 'Summary and Run' screen does not either generate a runSPADE.R file or run SPADE itself. This is also the case with actual FCS files that we have generated. What am I missing? Is the use of the Cytospade plugin documented outside the R vignette?

[Scott8586]

I am having the same issue - R 3.1, Cytoscape 2.8.3. There isn't a premade package for R 3.1, but I was able to install from source without error. dbottomly - have you made any progress?

[zbjornson]

Please see issue #91. We're working on it. Sorry!

(Closing as duplicate.)