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

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