CyTOForum

Hi all,

It appears Mac FlowJo v10 can now integrate SPADE.

http://docs.flowjo.com/vx/advanced-feat ... de-flowjo/

I have not tried this yet, so I cannot comment on how well it works. In theory though, I think this should allow you to do more FlowJo analysis on specific nodes.

However, it is unlikely to allow you to drop NEW files into the existing analysis.


Mike

The use of this is a bit problematic at the moment.
This is a workaround that runs SPADE on R, and presents the results using Cytoscape.
However, the latest SPADE version is incompatible with Cytoscape, requiring downgrading of all the components, including R itself.

Other than this and Cytobank, is there any other way to run SPADE?

Ron

To my knowledge, the only SPADE options are: Cytobank, stand-alone in Cytoscape, and running directly in R (which, at least in some R/SPADE/Cytoscape configurations, can then be visualized in Cytoscape using the contents of the "output" file).

What program errors are you getting with SPADE?

Hi Ron,
You can download SPADE from Peng Qiu's webpage. Click the software link to the left. From my understanding academic institutions can use it without a Stanford license, you may want to check that. I'm non-academic so I haven't tried it yet.
I got the page from this response thread on the Purdue site.
Rob

Thanks Rob, the script from Peng Qiu's page seems to work perfectly!

Mike - When running the newer version of SPADE through Flowjo/R, the results tree is made out of blank rectangles, and is completely uninterpretable.
A Flowjo representative tried to find a workaround by downgrading R and SPADE, but I have not been able to make it work properly.

Hi Ron,

Thanks for the updates,both regarding Peng Qiu's MATLAB iteration, and SPADE in FlowJo....good to know.

Hi folks, I just registered and saw this thread so with my FlowJo developer hat on, I'll comment that R integration is a pretty active project at the moment. Currently only FlowMeans works with any reliability.

Maciej of FlowJo