[BioC] annaffy annotation problem (hgu133plus2)

Glynn, Earl EFG at Stowers-Institute.org
Tue Apr 5 17:05:33 CEST 2005

> 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)

> i am wondering how the annotation of the Affymetrix chips are done...
> 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
> 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?

According to this page
Affymetrix updated its HG-U133_Plus_2 Annotations files a few days ago.
The CSV file version of the annotations was updated on 1 April 2005. I'm
not sure why Affy updated the BLASTP Annotation file on 1 April 2005 but
the BLASTX file supposedly hasn't been updated since 23 June 2004.  The
CSV annotations file gives the known mappings to various other data
sources for all the probesets on a GeneChip.

Annotation information on some of the probesets changes during every
update from Affy.  Sometimes probes that were mapped to known genes no
longer have that mapping, and with new information (presumably) some
unannotated probesets are given new information.

I would assume that the NetAffx information would be the same as these
annotations files?  Does anyone know if NetAffx information is
continuously updated and these annotations files are only updated
periodically, or should the information be the same from either Affy

I have worked mostly with various mouse GeneChips and Affy seems to
update them about every quarter, but I cannot get anyone at Affy to
state what their update cycle really is.  I have not used annaffy much
yet, but I'm curious how soon after the updates appear on the Affy web
site does this information show up in the annaffy package?

For the last year or so I've been loading these Affy CSV annotation
files for certain mouse chips into an Access database and trying to
track what changes Affy is making to their files:
The contents of these files seems to have stabilized after changing
considerably between Affy updates a year ago.  However, in the most
recent update (last week), the "LocusLink" field was renamed to "Entrez
Gene" in MOE430A but was still "Locuslink" in Mouse430_2.  It is
frustrating that Affy doesn't explain changes it makes to these files,
and one must reverse engineer the contents of the files and compare old
with new for every update.

Affy doesn't give much explanation of the various annotation fields on
their page, but the information there is useful:

Probe Set Data in Tabular Format

Exactly how Affy connects their probesets to the other data sources via
their Annotations file is still a bit of a mystery to me.

I'm curious where Affy's "Annotation Date" is in the data provided by

Earl F. Glynn    
Scientific Programmer
Stowers Institute for Medical Research

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