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Question: ReadAffy Error
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gravatar for Markus Schmidberger
11.3 years ago by
Markus Schmidberger380 wrote:
Hello, the ReadAffy function is no longer working on my windows machine. This code was working last week (and still on my linux system), then I installed Rtools (http://www.murdoch-sutherland.com/Rtools/), now I get an error. (I think I changed nothing else) library(affy); path <- "Z:/Microarray/hgu133a-spikein/rawdata" celFile <- list.celfiles(path=path,full.names=TRUE); affyBatch <- ReadAffy(filenames=celFile[1:3]); Fehler in int.unzip(file.path(path, zipname), topic, tmpd) : 'destination' existiert nicht The vector celFile is made up celFiles, no zip files. The data used, are CEL files from affycomp >traceback() 23: zip.file.extract(file, "Rdata.zip") 22: data(mapCdfName, envir = environment()) 21: cleancdfname(cdfname, addcdf = FALSE) 20: .nextMethod(.Object, ...) 19: eval(expr, envir, enclos) 18: eval(call, callEnv) 17: callNextMethod(.Object, ...) 16: .local(.Object, ...) 15: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 14: eval(expr, envir, enclos) 13: eval(call, callEnv) 12: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 11: .local(.Object, ...) 10: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 9: eval(expr, envir, enclos) 8: eval(call, callEnv) 7: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 6: .local(.Object, ...) 5: initialize(value, ...) 4: initialize(value, ...) 3: new("AffyBatch", exprs = exprs, cdfName = cdfname, phenoData = phenoData, nrow = dim.intensity[1], ncol = dim.intensity[2], annotation = cleancdfname(cdfname, addcdf = FALSE), description = description, notes = notes) 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, description = l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, sd = sd, cdfname = cdfname) 1: ReadAffy(filenames = celFile[1:3]) > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: affy affyio Biobase "1.14.2" "1.4.1" "1.14.1" Best Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
ADD COMMENTlink modified 11.3 years ago by Sylvia.Merk@ukmuenster.de60 • written 11.3 years ago by Markus Schmidberger380
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gravatar for Sylvia.Merk@ukmuenster.de
11.3 years ago by
Hi Markus, I think the problem lies in the way you define the path. When I remember some earlier experiences with R on windows you should use something like path <- "z:\\\\Microarray\\hgu133-spikein\\rawdata" What happens when you change to the cel-file-directory and use ReadAffy()? Best, Sylvia -- ??????????????????????????????????????????????????? Dr. Sylvia Merk Department of Medical Informatics & Biomathematics University of Muenster Domagkstr. 9 D-48149 Muenster Tel.: ++49-251-83-52498 Fax: ++49-251-83-55277 http://imib.uni-muenster.de/med_informatik.html Am Montag, den 03.09.2007, 08:26 +0200 schrieb Markus Schmidberger: > Hello, > > the ReadAffy function is no longer working on my windows machine. This > code was working last week (and still on my linux system), then I > installed Rtools (http://www.murdoch-sutherland.com/Rtools/), now I get > an error. (I think I changed nothing else) > > library(affy); > path <- "Z:/Microarray/hgu133a-spikein/rawdata" > celFile <- list.celfiles(path=path,full.names=TRUE); > affyBatch <- ReadAffy(filenames=celFile[1:3]); > > Fehler in int.unzip(file.path(path, zipname), topic, tmpd) : > 'destination' existiert nicht > > The vector celFile is made up celFiles, no zip files. The data used, are > CEL files from affycomp > > >traceback() > 23: zip.file.extract(file, "Rdata.zip") > 22: data(mapCdfName, envir = environment()) > 21: cleancdfname(cdfname, addcdf = FALSE) > 20: .nextMethod(.Object, ...) > 19: eval(expr, envir, enclos) > 18: eval(call, callEnv) > 17: callNextMethod(.Object, ...) > 16: .local(.Object, ...) > 15: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) > 14: eval(expr, envir, enclos) > 13: eval(call, callEnv) > 12: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) > 11: .local(.Object, ...) > 10: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) > 9: eval(expr, envir, enclos) > 8: eval(call, callEnv) > 7: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) > 6: .local(.Object, ...) > 5: initialize(value, ...) > 4: initialize(value, ...) > 3: new("AffyBatch", exprs = exprs, cdfName = cdfname, phenoData = > phenoData, > nrow = dim.intensity[1], ncol = dim.intensity[2], annotation = > cleancdfname(cdfname, > addcdf = FALSE), description = description, notes = notes) > 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, > description = l$description, notes = notes, compress = compress, > rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, > verbose = verbose, sd = sd, cdfname = cdfname) > 1: ReadAffy(filenames = celFile[1:3]) > > > sessionInfo() > R version 2.5.1 (2007-06-27) > i386-pc-mingw32 > locale: > LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONET ARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "methods" "base" > other attached packages: > affy affyio Biobase > "1.14.2" "1.4.1" "1.14.1" > > Best > Markus >
ADD COMMENTlink written 11.3 years ago by Sylvia.Merk@ukmuenster.de60
Hi, no, then there is the error: celFile <- list.celfiles(path="z:\\\\Microarray\\hgu133-spikein\\rawdata",full.na mes=TRUE); Warning message: list.files: 'Z:\\Microarray\hgu133-spikein\rawdata' ist kein lesbares Verzeichnis in: list.files(...) I think it is not a path problem. list.celfiles generates the right vector with Cel files. Best, Markus Sylvia Merk schrieb: > Hi Markus, > > I think the problem lies in the way you define the path. > When I remember some earlier experiences with R on windows you should > use something like > > path <- "z:\\\\Microarray\\hgu133-spikein\\rawdata" > > What happens when you change to the cel-file-directory and use > ReadAffy()? > > Best, > Sylvia > > > > -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599
ADD REPLYlink written 11.3 years ago by Markus Schmidberger380
Hi, I could solve my problem. I had wrong user rights for the WINDOWS/TEMP directory. So R could not write to this directory. Now my R user has read AND write rights for the directory and ReadAffy is working again. Best Markus Sylvia Merk schrieb: > Hi Markus, > > I think the problem lies in the way you define the path. > When I remember some earlier experiences with R on windows you should > use something like > > path <- "z:\\\\Microarray\\hgu133-spikein\\rawdata" > > What happens when you change to the cel-file-directory and use > ReadAffy()? > > Best, > Sylvia > > > > -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599
ADD REPLYlink written 11.3 years ago by Markus Schmidberger380
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