[BioC] AnnBuilder problem with custom List of genes

[claudio.is at libero.it]

this is the top of my input file

"A25"   "AA415819"
"A26"   "AA474746"
"A27"   "AA473306"
"A28"   "AA545607"
"A29"   "AA413090"
"A30"   "AA386616"
"A31"   "AA437482"
"A32"   "AA412921"
"A33"   "AI508650"
"A34"   "AA386794"

is it correct?


---------- Initial Header -----------

>From      : "Marc Carlson" mcarlson at fhcrc.org
To          : "claudio.is at libero.it" claudio.is at libero.it
Cc          : "jzhang" jzhang at jimmy.harvard.edu,"bioconductor" bioconductor at stat.math.ethz.ch
Date      : Thu, 16 Aug 2007 15:02:03 -0700
Subject : Re: [BioC] AnnBuilder problem with custom List of genes







> claudio.is at libero.it wrote:
> > here it is. thanks
> >
> >
> > R version 2.5.1 (2007-06-27) 
> > x86_64-unknown-linux-gnu 
> >
> > locale:
> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets" 
> > [7] "methods"   "base"     
> >
> > other attached packages:
> > AnnBuilder   annotate        XML    Biobase        GEM 
> >   "1.14.0"   "1.14.1"    "1.9-0"   "1.14.1"    "1.0.0" 
> >
> >
> >
> > ---------- Initial Header -----------
> >
> > >From      : "John Zhang" jzhang at jimmy.harvard.edu
> > To          : bioconductor at stat.math.ethz.ch, claudio.is at libero.it
> > Cc          : 
> > Date      : Thu, 16 Aug 2007 13:52:41 -0400 (EDT)
> > Subject : Re: [BioC] AnnBuilder problem with custom List of genes
> >
> >
> >
> >
> >
> >
> >
> >   
> >>> I am trying to build up an annotation package for an old chips for which there 
> >>>       
> >> is no annotation in BioC. I'am looking for AnnBuilder. First I create a file 
> >> GEM.txt, with two columns, the first corresponds to probe location on the array 
> >> (univocal numbers); the second corresponding to gene accession numbers.
> >>
> >>
> >> You need to provide more information (e. g. your R and BioC version numbers (try 
> >> sessionInfo()) and a few lines of your baseFile - GEM.txt). 
> >>
> >>     
> >>> then I applied the following script.
> >>>
> >>> library(AnnBuilder)
> >>>
> >>> myBaseType <- "gb"
> >>>
> >>> mySrcUrls <- getSrcUrl("all", "Mus musculus")
> >>>
> >>> myDir <- "GEM_annotation"
> >>>
> >>> ABPkgBuilder(baseName = "GEM.txt", srcUrls = mySrcUrls, baseMapType 
> >>>       
> >> =myBaseType, pkgName = "GEM",pkgPath = myDir, organism = "Mus musculus", version 
> >> = "1.0.0",author = list(authors = "joe", maintainer ="joe.joe at gmail.com"), 
> >> fromWeb = TRUE)
> >>     
> >>> after the creation of the package there is a little error in the DESCRIPTION 
> >>>       
> >> file that is easly solved. The problem appears after the installation and the 
> >> load of the package: actually no annotation is done. I get get following 
> >> results.
> >>     
> >>>> GEM()
> >>>>         
> >>> Quality control information for  GEM 
> >>> Date built: Created: Thu Aug 16 14:22:57 2007  
> >>>
> >>> Number of probes: 8734 
> >>> Probe number missmatch: None 
> >>> Probe missmatch: None 
> >>> Mappings found for probe based rda files: 
> >>>         GEMACCNUM found 8734 of 8734
> >>>         GEMCHRLOC found 0 of 8734
> >>>         GEMENTREZID found 0 of 8734
> >>>         GEMENZYME found 0 of 8734
> >>>         GEMPATH found 0 of 8734 
> >>> Mappings found for non-probe based rda files:
> >>>         GEMCHRLENGTHS found 21
> >>>         GEMORGANISM found 1
> >>>         GEMPFAM found 0
> >>>         GEMPROSITE found 0 
> >>>
> >>> Any suggestion??
> >>>
> >>> --
> >>> Claudio Isella
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor at stat.math.ethz.ch
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives: 
> >>>       
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >> Jianhua Zhang
> >> Department of Medical Oncology
> >> Dana-Farber Cancer Institute
> >> 44 Binney Street
> >> Boston, MA 02115-6084
> >>
> >>     
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >   
> Hi Claudio,
> 
> I cannot seem to reproduce this problem.  Would you mind giving us a few
> of your accession numbers too?
> 
>     Marc
>