[BioC] AnnBuilder problem with custom List of genes

John Zhang jzhang at jimmy.harvard.edu
Thu Aug 16 19:52:41 CEST 2007

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

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