[BioC] introduction - flowCore user

Thu Jan 22 15:28:13 CET 2009

Hi Nolwenn,

Thank you for your response.  I reinstalled packages lattice, latticeExtra
and flowViz, then went through the tutorial again.  Plot(x) still returns
the same 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
'print'

seesionInfo() returns:

R version 2.8.1 (2008-12-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tools     tcltk     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] flowViz_1.6.1      latticeExtra_0.5-4 lattice_0.17-20
RColorBrewer_1.0-2
 [5] flowCore_1.8.0     Biobase_2.2.1      feature_1.2.0      ks_1.5.10

 [9] rpanel_1.0-5       KernSmooth_2.22-22 rrcov_0.4-08       pcaPP_1.5

[13] mvtnorm_0.9-4      robustbase_0.4-5  

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.4.2 cluster_1.11.12     DBI_0.2-4          
[4] geneplotter_1.20.0  graph_1.20.0        grid_2.8.1         
[7] MASS_7.2-45         RSQLite_0.7-1       stats4_2.8.1       

---

To elaborate on my second question, let us say that I have a single FCS 2.0
file located at: 
C:\Documents and Settings\Owner\Desktop\Data\filename.fcs

And a folder of FCS 2.0 files located at: 
C:\Documents and Settings\Owner\Desktop\Data

Can I extract this data folder as a flowSet?  If so, where and in what
format do I plug the folder location information into:

fcs.loc <- system.file("extdata",package="flowCore")
file.location <- paste(fcs.loc, dir(fcs.loc), sep="/")
samp <- read.flowSet(file.location[1:3])  

Thanks again,

Stevan Lauriault
Founder, President and C.E.O.
Lauritech Inc. 
steve at lauritech.com
www.lauritech.com
t/f: (416)283-4066

Lauritech Inc.

-----Original Message-----
From: Nolwenn Le Meur [mailto:nlemeur at irisa.fr] 
Sent: Thursday, January 22, 2009 3:36 AM
To: stevan at lauriault.com
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] introduction - flowCore user

Steve Lauriault wrote:
> 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
> 'print'
>
> 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.
>
> Thanks,
>
> Stevan Lauriault
>
> Founder
> Lauritech Inc. 
> steve at lauritech.com
> www.lauritech.com
> t/f: (416)283-4066
>   
>  
>  
>
>   
> ------------------------------------------------------------------------
>
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http://news.gmane.org/gmane.science.biology.informatics.conductor
Hi Steve,

I thank you for your interest in the flowCore suite.

Recent improvements have been done in the lattice, latticeExtra and 
flowViz packages (used by flowCore for plotting) and you should probably 
update those to be able to use the plot function that use the splom method.

By the way, when reporting error messages, I would recommend that you 
send in our emails the output of the sessionInfo() command so we can see 
what version of R and associated packages you are using. More and more 
packages have dependencies and the version of each package is important. 
If you are using released R and bioC packages it evolves slowly (every 
6months) but it happens that major bugs need to be fixed within the 
6months. If you use development versions it can be very unstable.

I am not sure I get your second question but I am going to try to 
answer. You should be able to read batch of FCS2 and 3 files directly 
using the flowCore function read.flowSet. This will automatically 
generate a flowSet object:
fcs.loc <- system.file("extdata",package="flowCore")
file.location <- paste(fcs.loc, dir(fcs.loc), sep="/")
samp <- read.flowSet(file.location[1:3])

See flowSet man page for more details.

Best regards,
Nolwenn Le Meur

-- 
Nolwenn Le Meur, PhD
INSERM/IRISA - Equipe Symbiose 
Universite de Rennes I
Campus de Beaulieu
35042 Rennes cedex - France
Phone: +33 2 99 84 71 00
Fax: +33 2 99 84 71 71
E-mail: nlemeur at irisa.fr
Web: http://www.irisa.fr/symbiose/nolwenn_le_meur