[BioC] AnnBuilder problem with custom List of genes

[John Zhang]

>
>
>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
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084