[BioC] pdInfoBuilder: coreMps

[Benilton Carvalho]

If you update to R-2.15.0 (the current one), you can install the
annotation package with:

biocLite('pd.aragene.1.1.st')

http://www.bioconductor.org/packages/2.10/data/annotation/html/pd.aragene.1.1.st.html

best, b

On 10 May 2012 14:41, Mike Walter <michael_walter at email.de> wrote:
>
>   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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