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March 31, 2014

Comments

Aaron

That's pretty cool!

maciej

you should see it shred on a SSD datacenter box with 32 CPUs Aaron, and I've decoupled FJ from the "F" part so any data goes in now :) Although I have a post-cyto todo on acoustic data..

Anyway how's Switzerland? Stop by some time :)

Patrick Oltmann

I don't understand your issue with parallelizing calculations under R: This is pretty straight-forward and reasonably fast using "mcapply", you don't need FJ for that. Also compensation is quite easy when using with flowCore, assuming that your cytometer stores the compensation matrix as SPILL parameter. The only thing left is setting the gates themselves, which is - admittedly - not so nice without a GUI. Which brings me to the question: Is there any way to export gates from FJ in an XML-based format like Gating-ML?

maciej

Patrick,

I'll look into your suggestions, I mostly did it for the convenience of having draggable R scripts that integrate into a tool I'm familiar with. If I were an R buff, I'd probably be fluent in gating and compensation and all that :P but I'm not.

I think if you save as ACS file from Vx (not an option with V9) it includes XML stubs for each gate in the container. I will test this tomorrow.

In V9, you can save as XML, but there is no schema for that version's xml output to my knowledge. However, one of the bugs currently assigned to me is to improve reading of Jo files in Vx, so soon there's the laundry option (open V9 in Vx and then save as ACS to gain GateML stubs.)

Let me know if I got near to answering your question, or missed it - simm at treestar dot com

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