[BioC] introduction - flowCore user

Steve Lauriault stevan at lauriault.com
Thu Jan 22 00:42:46 CET 2009

Dear Members,

My name is Stevan Lauriault.  I am a flow cytometrist by trade, and I’m just
beginning to access R, flowCore and related packages for the purpose of
learning, accessing a good free analysis platform, and perhaps contributing
some insight/ideas to developers.  

I have a good background with FlowJo, CellQuest Pro, and FCS Express
software packages/features but am very new to open source development.  I'm
interested in high throughput quantitative imaging (and classical) flow
cytometry, population comparison algorithms, clustering/filtering and batch
statistical export/analysis.  

I’m currently going through the "HowTo_flowCore.pdf" document, and in
section 2.1.3 the plot(x) function returns the error:

Error in UseMethod("splom") : no applicable method for "splom" Error in
print(splom(x, pch = pch, ...)) : 
error in evaluating the argument 'x' in selecting a method for function

I have been told that splom now uses panel.xyplot.flowframe.  How do I
correct this error?

Also, this is probably a very easy question.  I am running R/flowCore on
Pentium4/Windows XP, and I'd like to know what annotation I should use to
extract FCS (2, 3, or looking forward... 4) files of a designated dos
filepath from my C:\ drive and read into the read.FCS function?  For
example, what format do I substitute for file.name in the function
read.FCS(file.name).  How then do I retrieve a series of FCS files and apply
them to flowSet?  

Any help would be appreciated.


Stevan Lauriault

Lauritech Inc. 
steve at lauritech.com
t/f: (416)283-4066

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