ReadAffy Error
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@markus-schmidberger-2240
Last seen 7.1 years ago
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
Annotation ExperimentData cdf affy affyio Annotation ExperimentData cdf affy affyio • 1.2k views
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@sylviamerkukmuensterde-1608
Last seen 7.1 years ago
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 >
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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
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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
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