[BioC] flowCore workflows and logical operations on gate views

[Wong, Chao-Jen]

Hi, Alessandro,

What kind of filter you are going to apply to wf[["Lymphocytes+"]] or wf[["Monocytes-"]]?  There are four types of actions you can apply to a work flow object. They are compensation, transformation (logicle, asinh, and etc.), normalization, and gating/filtering (rectangleGate, rangeGate, norm2Filter, kmeansFilter and etc.) actions. As long as your filtering actions are in these categories, and then of course you can apply them to any of the gate views (by specifying the "parent" argument). There are some extra gating/filtering actions implemented in the flowStats packages that you might find useful. 


Chao-Jen

----- Original Message -----
From: "Alessandro Di Cara" <rmailing at di-cara.com>
To: bioconductor at r-project.org
Sent: Thursday, February 3, 2011 2:38:13 PM
Subject: [BioC] flowCore workflows and logical operations on gate views

Dear List,

I am using the flowCore and flowViz packages to perform some flow 
cytometry analyses on clinical data.
I find the packages extremely useful.

Some of the gating strategies I have to implement are quite tricky and I 
would like to use the "Work Flows" system
described in the flowCore reference manual. So far, I find this approach 
very efficient, not only for accessing the intermediate analysis steps 
of my analysis but also for solving memory issues when loading many FCS 
files.

I am stuck with the implementation of logical operations on the gate 
views of a workflow

For example let's say  I have a workflow object "wf" with two gate views

wf[["Lymphocytes+"]]
wf[["Monocytes-"]]

I would like to apply a filter on cells that are in the 
wf[["Lymphocytes+"]] OR wf[["Monocytes-"]] gate views.

Can this be done using the work flows system?  Would these operations be 
reflected in the work flow graph plot ?

Thank you in advance for you help

All the best,

Alessandro Di Cara
/

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-- 
Chao-Jen Wong 
Program in Computational Biology 
Division of Public Health Sciences 
Fred Hutchinson Cancer Research Center 
1100 Fairview Avenue N., M1-B514 
PO Box 19024 
Seattle, WA 98109 
206.667.4485 
cwon2 at fhcrc.org