[BioC] pdInfoBuilder: coreMps

[Mike Walter]

   Dear List,
   I have a set of the new AraGene 1.1-st arrays and thus like to build a
   corresponding pdInfo package. Anyway, I get an error while creating the
   package. Please see code and error mesasge below. Obviously, the mps file
   for the array can't be found, and I was unable to figure out how to specify
   the  file location in the new("AffyGenePDInfoPkgSeed", ... ) function.
   Looking through the vignette, archive and help files I never came across the
   mps message, so any suggestion on how to specify the file (which is also in
   the working directory).
   Thank you very much in advance,
   Michael
   baseDir = "F:/Auswertung/Array Annotationen/Affy"
   > (pgf <- list.files(paste(baseDir,
   "MO_AraGene-1_1-st-v1_strip_libraryfile",  sep="/"), pattern = ".pgf",
   full.names = TRUE))
   [1] "F:/Auswertung/Array
   Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene-1_1-st.pgf"
   > (clf <- list.files(paste(baseDir,
   "MO_AraGene-1_1-st-v1_strip_libraryfile",  sep="/"), pattern = ".clf",
   full.names = TRUE))
   [1] "F:/Auswertung/Array
   Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene-1_1-st.clf"
   > (prob <- list.files(baseDir, pattern = "tair10.probeset.csv",full.names =
   TRUE))
   [1] "F:/Auswertung/Array
   Annotationen/Affy/AraGene-1_1-st-v1.na32.tair10.probeset.csv"
   > (trans = list.files(baseDir, pattern = "tair10.transcript.csv",full.names
   = TRUE))
   [1] "F:/Auswertung/Array
   Annotationen/Affy/AraGene-1_1-st-v1.na32.tair10.transcript.csv"
   > (core = list.files(paste(baseDir,
   "MO_AraGene-1_1-st-v1_strip_libraryfile",  sep="/"), pattern = ".mps",
   full.names = TRUE))
   [1] "F:/Auswertung/Array
   Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene-1_1-st.mps"
   >
   > seed <- new("AffyGenePDInfoPkgSeed",
   + pgfFile = pgf, clfFile = clf,
   + probeFile = prob, author = "Michael Walter",
   + transFile = trans,
   + email = "michael.walter at med.uni-tuebingen.de",
   + biocViews = "AnnotationData",
   + genomebuild = "TAIR10",
   + organism = "Arabidopsis", species = "Arabidopsis thaliana")
   >
   > makePdInfoPackage(seed, destDir = ".")
   ============================================================================
   ====
   Building annotation package for Affymetrix Gene ST Array
   PGF.........: AraGene-1_1-st.pgf
   CLF.........: AraGene-1_1-st.clf
   Probeset....: AraGene-1_1-st-v1.na32.tair10.probeset.csv
   Transcript..: AraGene-1_1-st-v1.na32.tair10.transcript.csv
   Core MPS....: coreMps
   ============================================================================
   ====
   Parsing file: AraGene-1_1-st.pgf... OK
   Parsing file: AraGene-1_1-st.clf... OK
   Creating initial table for probes... OK
   Creating dictionaries... OK
   Parsing file: AraGene-1_1-st-v1.na32.tair10.probeset.csv... OK
   Parsing file: coreMps... Fehler in file(file, "rt") : kann Verbindung nicht
   öffnen
   Zusätzlich: Warnmeldungen:
   1: In is.na(x) :
     is.na() auf nicht-(Liste oder Vektor) des Typs 'NULL' angewendet
   2: In is.na(x) :
     is.na() auf nicht-(Liste oder Vektor) des Typs 'NULL' angewendet
   3: In file(file, "rt") :
     kann Datei 'coreMps' nicht öffnen: No such file or directory
   >
   > sessionInfo()
   R version 2.14.0 (2011-10-31)
   Platform: i386-pc-mingw32/i386 (32-bit)
   locale:
   [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
   [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
   [5] LC_TIME=German_Germany.1252
   attached base packages:
   [1] stats     graphics  grDevices utils     datasets  methods   base
   other attached packages:
   [1] pdInfoBuilder_1.20.0 affxparser_1.26.4    RSQLite_0.11.1
   [4] DBI_0.2-5            oligo_1.18.1         oligoClasses_1.16.0
   [7] Biobase_2.14.0
   loaded via a namespace (and not attached):
   [1] affyio_1.22.0         Biostrings_2.22.0     bit_1.1-8
   [4] ff_2.2-6              IRanges_1.12.6        preprocessCore_1.16.0
   [7] splines_2.14.0        tools_2.14.0          zlibbioc_1.0.1
   >
   --
   Dr. Michael Walter
   MFT Services
   University of Tübingen
   Calwerstr. 7
   72076  Tübingen
   Tel.: +49 7071 29 83210
   Fax. + 49 7071 29 5228
   web: www.mft-services.de
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