[BioC] ReadAffy Error

[Sylvia Merk]

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_MONETARY=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
>