[BioC] pd.mapping 10Karray

[Marianne Tuefferd]

Dear all,

I would like to analyze 10K SNParray using oligo package.
I've first tried using makePDpackage() function as detailed previously
https://stat.ethz.ch/pipermail/bioconductor/2006-February/012078.html

> library("makePlatformDesign")
> cdfFile <- "Mapping10K_Xba142.CDF"
> csvAnno <- "Mapping10K_Xba142.na23.annot.csv"
> csvSeq <- "Mapping10K_probe_tab"
> makePDpackage(designFile=cdfFile, file1=csvseq,file2=csvannot
+ ,manufacturer="affymetrix",type="SNP",textCDF = TRUE )
Error in makePDpackage(designFile = cdfFile, file1 = csvseq, file2 =
csvannot,  :
        unused argument(s) (textCDF = TRUE)


Using pdInfoBuilder package I get the following error message.
Does anyone has a clue?

Thank you very much for your help,

Marianne


 > library("pdInfoBuilder")
 > pkg <- new("AffySNPPDInfoPkgSeed",
+            version = "0.0",
+            email = "tuefferd at vjf.inserm.fr",
+            biocViews = "AnnotationData",
+            cdfFile = cdfFile,
+            csvAnnoFile = csvAnno,
+            csvSeqFile = csvSeq)
 > makePdInfoPackage(pkg, destDir = ".")
Creating package in ./pd.mapping10k.xba142
Error in gsub(pattern, replacement, x, ignore.case, extended, fixed,
useBytes) :
    invalid argument
 > traceback()
7: gsub(nm[i], symbolValues[[i]], res)
6: subsFileName(tmp[length(tmp)])
5: cpSubs(src, dest)
4: copySubstitute(dir(originDir, full.names = TRUE), pkgdir, symbolValues,
        recursive = TRUE)
3: createPackage(pkgname = pkgName, destinationDir = destDir, originDir
= templateDir,
        symbolValues = syms, quiet = quiet)
2: makePdInfoPackage(pkg, destDir = ".")
1: makePdInfoPackage(pkg, destDir = ".")

 > sessionInfo()
R version 2.5.1 (2007-06-27)
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] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
makePlatformDesign
"1.0.0"
         pdInfoBuilder                 oligo BufferedMatrixMethods
               "1.0.0"             "1.0.2-3"               "1.0.0"
        BufferedMatrix                affyio            affxparser
               "1.0.0"               "1.4.0"               "1.8.0"
               RSQLite                   DBI               Biobase
               "0.5-6"               "0.2-3"              "1.14.0"