FAQ  •  Register  •  Login

FlowJov10, SPADE

Forum rules
Please be as geeky as possible. Reference, reference, reference.
Also, please note that this is a mixed bag of math-gurus and mathematically challenged, so choose your words wisely :-)
<<

mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Mon Feb 24, 2014 6:35 pm

FlowJov10, SPADE

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
<<

rrotkopf

Participant

Posts: 6

Joined: Mon Dec 02, 2013 11:51 am

Post Thu Apr 03, 2014 9:26 am

Re: FlowJov10, SPADE

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
<<

mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu Apr 03, 2014 3:16 pm

Re: FlowJov10, SPADE

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?
<<

robs

Contributor

Posts: 40

Joined: Mon Dec 02, 2013 3:42 pm

Location: University of Connecticut

Post Thu Apr 03, 2014 3:21 pm

Re: FlowJov10, 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
<<

rrotkopf

Participant

Posts: 6

Joined: Mon Dec 02, 2013 11:51 am

Post Sun Apr 06, 2014 8:23 am

Re: FlowJov10, SPADE

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.
<<

mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Mon Apr 07, 2014 3:17 pm

Re: FlowJov10, SPADE

Hi Ron,

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

maciej

Participant

Posts: 3

Joined: Thu May 15, 2014 4:46 pm

Post Tue May 20, 2014 3:59 pm

Re: FlowJov10, SPADE

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

Return to CyTOF data analysis

Who is online

Users browsing this forum: No registered users and 16 guests