[BioC] Importing OSX directory into read.flowSet()
Steve Lauriault
stevan at lauriault.com
Sun Jan 25 05:06:47 CET 2009
For future reference:
To read a Mac OSX directory into the flowSet function, you must omit the
"Macintosh HD" directory in filepath.
For instance, 14 FCS 2.0 files are found in "Data" directory on OSX desktop
(Macintosh HD/Users/stevan/Desktop/Data). To read files from "Data" into
the flowSet function:
> read.flowSet(path = "/Users/stevan/Desktop/Data", package = flowCore")
Can also use:
> read.flowSet(path = "~stevan/Desktop/Data", package = flowCore")
Regards,
Stevan
-----Original Message-----
From: Stevan Lauriault [mailto:stevan at lauriault.com]
Sent: Friday, January 23, 2009 3:43 PM
To: bioconductor at stat.math.ethz.ch
Cc: nlemeur at irisa.fr
Subject: [BioC] introduction - flowCore user
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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