[BioC] AnnBuilder problem with custom List of genes

[claudio.is at libero.it]

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
>