[BioC] introduction - flowCore user

Stevan Lauriault stevan at lauriault.com
Fri Jan 23 21:43:24 CET 2009


Thank you!

It seems the flowViz (splom) error doesn't occur when I run R-flowCore  
from My MacBook Pro setup (OSX 10.5.6):

 > sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1

locale:
en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8

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_0.17-17
  [4] RColorBrewer_1.0-2 flowCore_1.8.1     Biobase_2.2.1
  [7] feature_1.2.0      ks_1.5.10          mvtnorm_0.9-4
[10] rpanel_1.0-5       KernSmooth_2.22-22 rrcov_0.4-07
[13] robustbase_0.4-5

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.4.2 DBI_0.2-4           MASS_7.2-45
[4] RSQLite_0.7-1       cluster_1.11.11     geneplotter_1.20.0
[7] graph_1.20.0        grid_2.8.1          stats4_2.8.1

---

yet it continues to produce an error from XP (sessionInfo contained in  
previous email).


Also, with respect to the email just previous to this one; which  
annotation do I use to plug a MacBook Pro OSX filepath into:

amp <- read.flowSet(path="C:/Documents and Settings/Owner/Desktop/Data")

The OSX filepath, as far as I can tell is "Macintosh HD/Users/stevan/ 
Desktop/Data".

Cheers,

Steve
---
Stevan Lauriault
Founder
Lauritech, Inc.
steve at lauritech.com
416-283-4066




>
>
>
>
>
> -----Original Message-----
> From: Nolwenn Le Meur [mailto:nlemeur at irisa.fr]
> Sent: Thursday, January 22, 2009 2:30 PM
> To: stevan at lauriault.com
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] introduction - flowCore user
>
> Hi Steve,
>
> Thank you for point at the error. We need to fix the released  
> version of
> flowViz (I get the same error and have the same package version).  The
> development version works if you really want to test the function but
> you should be careful in mixing release and development versions as it
> may generate new errors that might more difficult to track.
>
> As for your second question if you want all the files from your "Data"
> directory, this should work:
>
> samp <- read.flowSet(path="C:/Documents and Settings/Owner/Desktop/ 
> Data")
>
>
> Hope it helps,
> Nolwenn
>
> Steve Lauriault wrote:
>> 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
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>>
>> 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
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