[BioC] introduction - flowCore user

Heidi Dvinge heidi at ebi.ac.uk
Thu Jan 22 23:40:53 CET 2009


Hi Steve,

> Hi Nolwenn,
>
> Your suggestion helped.  Thank you.  I needed a forward-slash instead of
> back-slash in the filepath.
>
>> x <- read.FCS("C:/Documents and
>> Settings/Owner/Desktop/Data/surface.002")
>> summary(x)
>
> Returns:
>
>         FSC-H  SSC-H    FL1-H    FL2-H  FL3-H   FL2-A     FL4-H
> Min.      114   11.0    1.000    1.000    1.0    0.00     1.000
> 1st Qu.   328  109.0    2.867    1.000  113.9    0.00     4.705
> Median    520  326.0  107.000    1.084  192.1    0.00    10.390
> Mean      546  418.2  975.900   13.160  238.2    2.47    58.890
> 3rd Qu.   716  677.0 1728.000    2.574  329.7    0.00    18.650
> Max.     1023 1023.0 8816.000 8203.000 7167.0 1023.00 10000.000
>
>
> And also:
>
>> read.flowSet(path="C:/Documents and Settings/Owner/Desktop/Data",
>> package
> = "flowCore")
>
> Returns:
>
> A flowSet with 14 experiments.
>
>   column names:
>   FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H
>
> However, when I input:
>
> fs <- read.flowSet(path="C:/Documents and Settings/Owner/Desktop/Data",
> package = "flowCore"), name.keyword = "SAMPLE ID", phenoData = list(name =
> "SAMPLE ID", Filename = "$FIL"))
>
It looks like your problem here is the closing ")" after
package="flowCore". When that's present, it's the end of the read.flowSet
function - and the comma is indeed unexpected.

HTH
\Heidi

> It returns:
>
> Error: unexpected ',' in "fs <- read.flowSet(path = "C:/Documents and
> Settings/Owner/Desktop/Data", package = "flowCore"),"
>
> When logic tells me that it should accept the comma and return:
>
> [1] "name" "Filename"
>
> Regards,
>
> Stevan Lauriault
> Founder, President and C.E.O.
> Lauritech Inc.
> steve at lauritech.com
> www.lauritech.com
> t/f: (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
> _______________________________________________
> 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



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