[BioC] Missing chromosomal locations in hgu133a package

[John Zhang]

>>>thanks for Your answer. I'm aware of the fact I could create annotation 
>>>packages on my own using AnnBuilder. However, the comparison I mentioned 
>>>was of GoldenPath data and annotation packages of about the same date 
>>>(mid 2005), and even current annotation packages show this discrepancy 
>>>in the number of chromosomal locations provided in hgu133a.  So I 
>>>wondered if there is some good reason to not provide chromosomal 
>>>locations for some probesets (e.g. unreliable mappings in GoldenPath) or 
>>>if this is because of special paths AnnBuilder uses to merge all sources.
>> 

There may be two reasons. 

1. AnnBuilder uses RefLink.txt and RefGene.txt from Golden Path for annotation. 
Location data were missing from the file for some of the genes/probes(ie. 
8847/216856_s_at) in a test run. Need to talk to Golden Path about htis. 

2. The base file used to build the annotation package may not be in sync with 
the current probe-GB mapping provided by AffyMetrix. Nianhua, do you know if a 
fresh download from AffyMetrix was used for release 1.8?





>> 
>> AnnBuilder does not make any decision on who gets mapped and who does not. I 
>> will have to step through the mapping process to tell you what might be the 
>> problem. Could you give me a few of the probes that are missed again?
>> 
>> Thanks.
>> 
>> 
>> 
>>>Regards,
>>>Hilmar
>>>
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>> 
>> 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
>> 
>
>-- 
>
>Hilmar Berger
>Studienkoordinator
>Institut für medizinische Informatik, Statistik und Epidemiologie
>Universität Leipzig
>Härtelstr. 16-18
>D-04107 Leipzig
>
>Tel. +49 341 97 16 101
>Fax. +49 341 97 16 109
>email: hilmar.berger at imise.uni-leipzig.de

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