[BioC] annaffy annotation problem (hgu133plus2)

[Dipl.-Ing. Johannes Rainer]

hi john,
i saw that they (=Affymetrix) updated their annotation files in the 
"SUPPORT" link on 1/04/05, so perhaps in this new version the gene is 
mapped correctly (i hope so).
cheers, jo


Quoting John Zhang <jzhang at jimmy.harvard.edu>:

>
>> Date: Mon, 4 Apr 2005 09:08:13 -0400 (EDT)
>> From: John Zhang <jzhang at jimmy.harvard.edu>
>> Subject: Re: [BioC] annaffy annotation problem (hgu133plus2)
>> To: johannes.rainer at tugraz.at
>> Cc: bioconductor at stat.math.echz.ch
>> MIME-Version: 1.0
>> Content-MD5: Fxd6ky8TXHI0BkXVe+JUCw==
>>
>>
>>> i am wondering how the annotation of the Affymetrix chips are done... i
>>> know how the AnnBuilder package works and i also used it, but as the
>>> starting point for any annotation is the GenBank id for which the probe
>>> set codes i would like to know from where this mapping information
>>> comes. are those packages built using the probe set to genbank mapping
>>> that can be downloaded from affymetrix, or the (sometimes) newer
>>> annotation that is available through Affymetrix NetAffx or some other
>>> source?
>>
>
> The mappings were downloaded from the Affymetrix's "SUPPORT" link. It 
> would be
> very useful if you could also inform Affymetrix about this error (and 
> any other
> errors).
>
> Thank you for reporting.
>
>>>
>>> I am really interested in this, because we got a little annotation
>>> problem with the annotation for the hgu133plus2 chip (version 1.7.0).
>>> one of our interesting genes in our study was the probe set 208078_s_at
>>> which is mapped using the hgu133plus2 package (and the annotation from
>>> Affymetrix) to NM_030751 (TCF8). we made real time PCR to confirm its
>>> regulation but this TCF8 was not regulated at all. so i went back to
>>> NetAffx tool and saw that Affymetrix gave a new annotation for this
>>> probe set, all 11 probes perfectly match with the gene NM_173354
>>> (SNF1LK) (i wonder how Affymetrix could annotate this gene to the TCF8
>>> gene).
>>>
>>> if the annotation packages are built using the downloadable probe set
>>> to genbank mapping files from Affymetrix (which may never updated and
>>> corrected for errors by Affymetrix) i believe that there may be more
>>> annotation errors in this package like the one we found.
>>>
>>> cheers, jo
>>>
>>> _______________________________________________
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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
>
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
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