[BioC] build Genome version

Marc Carlson mcarlson at fhcrc.org
Fri Mar 4 23:44:15 CET 2011

Hi Elodie,

I think you are asking about the probeset to gene mappings here.  And
the answer to this question is that it depends on what the manufacturer
did.  The bioconductor cdf, and .db packages are all based on
manufacturer provided mappings for this platform.  These are updated
every 6 months.  But, we do not know what the manufacturers process is
for deciding this.  If you trust Affymetrix, then I strongly suspect
that you don't care about this information (unless you plan to use the
CHRLOC mapping - see below) as it will be factored out when you run the
analysis.  If you do not trust Affymetrix to know what their probes are
measuring, then you should indeed look at the brain-array remapped

On the other hand, if you are not asking about the gene to probe
mappings and instead are asking about the CHRLOC positions mapped to
these genes in the .db package, those will be based on the most recent
build of the human genome, (which would be hg19).  You can see this
information by looking at the help page for the CHRLOC mapping.  If you
want to use the CHRLOC mapping and would like to use the older
annotations, I would NOT recommend using an old annotation package. 
Instead, I would learn to use the GenomicFeatures package, which will
allow you to get detailed genomic coordinate information for any gene
separately (once you have the entrez gene ID).

I hope this helps,


On 03/02/2011 04:09 AM, Elodie Chapeaublanc wrote:
> Hi, 
> I want to known that is the build genome version used in affymetrix CDF
> packages (e.g. : hgu133plu2cdf). 
> I guess in bioconductor 2.7,  the gemome build version is the last one : hg19
> GRCh37.
> I want to use the hg18 version. I think that I must used an old package
> version like bioconductor 2.6
> Thanks 
> Elodie
> --
> Elodie Chapeaublanc
> IE Bioinformatique
> Équipe Oncologie Moléculaire           
> Institut Curie - UMR 144 - CNRS               
> 26 rue d'Ulm - 75248 Paris Cedex 05  
> Tel: +33 1 56 24 63 57
> Email: elodie.chapeaublanc at curie.fr
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