[BioC] annotations for Codelink arrays

John Zhang jzhang at jimmy.harvard.edu
Fri Oct 14 14:37:09 CEST 2005

>1) In the case of MULTIPLE probes: Can AnnBuilder find when a  
>coherent mapping for different Genbank Accession numbers to Entrez  
>Gene exists and then use this mapping? or when it find two Genbank  
>acc. associated to one probe it avoids mapping at all?

When a probe is mapped to multiple Genbank Accession numbers (separated by a ";" 
in the base file), AnnBuilder tries to get the mappings of these GB numbers to 
Entrez ids using both UniGene and Entrez as the source and then figures out if 
the two sources agree. If they do not agree, the one with the smallest Entrez id 
is used. Based on my previous experience, the two sources usually agree except 
for ESTs that can only be mapped by UniGene.

>2) For the CODELINK_UNIQUE: Until we can get the mappings to Genbank  
>acc. Is there any possibility to use the mappings to Unigene?.

Yes, UniGene id can be used. Use "ug" for baseMapType when calling ABPkgBuilder.

>El 13/10/2005, a las 3:14, Robert Gentleman escribió:
>> Hi Tao,
>>   If the right set of mappings is available to get started, AnnBuilder
>> is pretty easy to use. We can help you with the first one or two, and
>> are happy to distribute them. If there is more widespread interest  
>> (and
>> they are stable) we can add them to the build process.
>>   Robert
>> Shi, Tao wrote:
>>> Any plans to create annotation packages for Codelink arrays?
>>> ...Tao
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> -- 
>> Robert Gentleman, PhD
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M2-B876
>> PO Box 19024
>> Seattle, Washington 98109-1024
>> 206-667-7700
>> rgentlem at fhcrc.org
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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

More information about the Bioconductor mailing list