[BioC] annaffy annotation problem (hgu133plus2)

[John Zhang]

>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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>
>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