introduction - flowCore user
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@steve-lauriault-3237
Last seen 7.8 years ago
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 ?? ? ?
Annotation flowCore Annotation flowCore • 1.6k views
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@nolwenn-le-meur-3238
Last seen 7.8 years ago
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
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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
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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
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On Thu, Jan 22, 2009 at 5:39 PM, Steve Lauriault <stevan at="" lauriault.com=""> wrote: > 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() gives you information about attached/loaded packages, not installed ones. To get a list of installed packages, try rownames(installed.packages()) You can attach a package using library(pkgname) (which may attach/load further packages). -Deepayan
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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 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@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 ADD REPLY 0 Entering edit mode 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