[BioC] pdInfoBuilder: coreMps
Mike Walter
michael_walter at email.de
Thu May 10 16:49:11 CEST 2012
Hi Benilton,
Thank you very much. I'll go and update my R Version.
Kind regards, Michael
--
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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Gesendet: Donnerstag, 10. Mai 2012 um 16:38 Uhr
Von: "Benilton Carvalho" <beniltoncarvalho at gmail.com>
An: "Mike Walter" <michael_walter at email.de>
Cc: bioconductor at r-project.org
Betreff: Re: [BioC] pdInfoBuilder: coreMps
If you update to R-2.15.0 (the current one), you can install the
annotation package with:
biocLite('pd.aragene.1.1.st')
[1]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: [2]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
> nded
> recipient, please contact the sender and delete the message. Any
unauthorize
> d
> use of the information contained in this message is prohibited.
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References
1. http://www.bioconductor.org/packages/2.10/data/annotation/html/pd.aragene.1.1.st.html
2. http://www.mft-services.de/
3. https://stat.ethz.ch/mailman/listinfo/bioconductor
4. http://news.gmane.org/gmane.science.biology.informatics.conductor
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