[BioC] pdInfoBuilder: coreMps

Mike Walter michael_walter at email.de
Thu May 10 15:41:53 CEST 2012

   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,
   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
   > (clf <- list.files(paste(baseDir,
   "MO_AraGene-1_1-st-v1_strip_libraryfile",  sep="/"), pattern = ".clf",
   full.names = TRUE))
   [1] "F:/Auswertung/Array
   > (prob <- list.files(baseDir, pattern = "tair10.probeset.csv",full.names =
   [1] "F:/Auswertung/Array
   > (trans = list.files(baseDir, pattern = "tair10.transcript.csv",full.names
   = TRUE))
   [1] "F:/Auswertung/Array
   > (core = list.files(paste(baseDir,
   "MO_AraGene-1_1-st-v1_strip_libraryfile",  sep="/"), pattern = ".mps",
   full.names = TRUE))
   [1] "F:/Auswertung/Array
   > 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
   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)
   [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
   Confidentiality Note:
   This message is intended only for the use of the named recipient(s) and may
   contain confidential and/or proprietary information. If you are not the inte
   recipient, please contact the sender and delete the message. Any unauthorize
   use of the information contained in this message is prohibited.

More information about the Bioconductor mailing list