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nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
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Can't cluster flow cytometry data on all channels #114

Closed Dawsondmg closed 9 years ago

Dawsondmg commented 9 years ago

Not all of the fluorescence channels appear on the parameter selection box after I select calculate SPADE in FlowJo. Is there some way to fix this? Also, if I'm analyzing a SPADE tree in Cytoscape, is it possible to gate on the actual plot within Cytoscape?

Thanks!

zbjornson commented 9 years ago

Hello,

Please contact FlowJo support about that question. They integrated our open-source package and we don't know if they modified it in a way that would cause this. However, note that only channels that are common to all of your FCS files can be used for clustering. Perhaps that is what you're encountering.

In Cytoscape, you cannot gate on the plot. Selecting nodes shows the events from those nodes in the plot (opposite of what you're asking).

Best, Zach

Dawsondmg commented 9 years ago

Thanks Zach! I'll contact FlowJo. Also, is it correct that one can circumvent FlowJo by using R and Cytospade to generate the output files for analysis in Cytoscape?

Thanks again, Dawson

zbjornson commented 9 years ago

Hi Dawson, Our Cytoscape plugin is currently broken. If you are comfortable with the basics of R, you can run SPADE entirely from R. The tutorial walks through most of the steps. The final alternative is using Cytobank. It is a paid feature but I think free 30-day trials are available. Zach