openCyto transitional gate
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 22 days ago
(Private Address)
Niclas,

Try this:

gating_method: flowClust

gating_args: transitional=TRUE

see "help(flowClust.2d)" for more details.

Mike

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On 04/09/2015 02:47 AM, Niclas Thomas wrote:

Hi Mike and Greg,

Sorry to bother you again - I've contacted you previously about flowStats.

My question this time is about openCyto - I simply want to gate transitional B cells using CD38 and IgM. In your publication and on your vignette here http://opencyto.org/openCytoVignette.html you mention that there exists a gate specifically for transitional B cells. I've gone through the manuals and also the source code on GitHub and can't find the relevant section to help me define this transitional gate in my template csv file.

I was just wondering if you'd be able to tell me how to do this e.g. I've tried various incarnations of

alias pop parent dims gating_method gating_args collapseDataForGating groupBy preprocessing_method preprocessing_args

 

trans trans Bcells CD38,IgM transitional          
trans trans Bcells CD38,IgM transitionalBcells          


etc. but nothing seems to register as the correct name for the gating_method.

Thanks for your help.

Nic

Niclas Thomas PhD,
UCL Genetics Institute,
Darwin Building Room 212,
Gower Street,
London,
WC1E 6BT
niclas.thomas@ucl.ac.uk

 

flow cytometry opencyto • 888 views
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