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Markus Schmidberger
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380
@markus-schmidberger-2240
Last seen 10.2 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
