[BioC] AnnBuilder problem with custom List of genes

[claudio.is at libero.it]

Dear BioC,


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.

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