[BioC] annaffy annotation problem (hgu133plus2)

aedin culhane Aedin.Culhane at ucd.ie
Mon Apr 4 17:02:06 CEST 2005

Hi Johannes
Maybe have a look at the EnsEMBL, EnsMart annotation. It permits 
visualization of the probe matches to the sequence which can be handy. 

I think your probe matches to:  

You'll prob need to follow the Affy links out from there, 
Hope this is useful

>Message: 9
>Date: Mon, 04 Apr 2005 10:28:00 +0200
>From: "Dipl.-Ing. Johannes Rainer" <johannes.rainer at tugraz.at>
>Subject: [BioC] annaffy annotation problem (hgu133plus2)
>To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>Message-ID: <20050404102800.4zxbhgwaqoccko8o at webmail.tugraz.at>
>Content-Type: text/plain;	charset=ISO-8859-1;	format="flowed"
>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 
>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 
>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
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>End of Bioconductor Digest, Vol 26, Issue 4

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