[BioC] AnnBuilder problem with custom List of genes

[Marc Carlson]

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
>>
>>     
>
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>
>   
Hi Claudio,

I cannot seem to reproduce this problem.  Would you mind giving us a few
of your accession numbers too?

    Marc