Thank you Deepayan, Would anyone happen to know why I have just lost all of my recently installed packages? Is there a way to quickly retrieve the ones I had and/or prevent this from happening again in the future? > sessionInfo() 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] stats graphics grDevices utils datasets methods base > See below email for previously installed packages. Regards, Stevan -----Original Message----- From: Deepayan Sarkar [mailto:deepayan.sarkar@gmail.com] Sent: Thursday, January 22, 2009 6:56 PM To: Nolwenn Le Meur Cc: stevan at lauriault.com; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] introduction - flowCore user On Thu, Jan 22, 2009 at 11:29 AM, Nolwenn Le Meur <nlemeur at="" irisa.fr=""> wrote: > 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. The version being installed does not have the R/splom.R file, even though the version in SVN does. It looks like the version was not updated after splom.R was added, so a new tarball was not built. Should be fixed in a few days. -Deepayan

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.FCSfile.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