[BioC] Missing chromosomal locations in hgu133a package
jzhang at jimmy.harvard.edu
Fri Jul 21 22:38:26 CEST 2006
>>>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?
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>>>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
>Institut für medizinische Informatik, Statistik und Epidemiologie
>Tel. +49 341 97 16 101
>Fax. +49 341 97 16 109
>email: hilmar.berger at imise.uni-leipzig.de
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
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