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 ?quipe Oncologie Mol?culaire 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

Hi Elodie, I am not sure what the official genome version is for hgu133plus2cdf, but if you are interested in using hg18 I would suggest you use the custom cdf files form the brainarray group: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF _download.asp They have a cdf for different genome versions, and the cdf are more accurate because they have remapped the probes at each genome version and filtered for problematic probes. Hope that helps, Fong On Wed, Mar 2, 2011 at 4:09 AM, Elodie Chapeaublanc < Elodie.Chapeaublanc@curie.fr> 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@curie.fr > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

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 annotations. 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, Marc 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 > ?quipe Oncologie Mol?culaire > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >