On Thu, Feb 4, 2010 at 9:29 AM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Axel, > > axel.klenk at actelion.com wrote: >> >> Dear BioC list and Biocore Data Team, >> >> we are using various Agilent arrays and the recent paper by Gertz et al. >> ( http://www.biomedcentral.com/1471-2164/10/566 ) made me feel a >> little bit uneasy about the annotation provided by that vendor. >> >> As far as I understand, BioC annotation, e.g. in package hgug4112a.db, >> is using EntrezGene IDs as keys to retrieve public annotation for a given >> EntrezGene entry -- but where does the mapping from Agilent's Oligo ID >> to EntrezGene come from? > > The first mapping is usually vendor --> Entrez Gene using the manufacturer's > annotation data. However, in this case, it appears that the mapping was > vendor --> GenBank and then all other mappings were from GenBank. From > ?hgug4112aACCNUM: > > For chip packages such as this, the ACCNUM mapping comes directly from the > manufacturer. This > is different from other mappings which are mapped onto the probes via an > Entrez Gene identifier. > >> >> I have tried to find the answer in the package's reference manual and help >> pages but would prefer to be absolutely sure in this case... >> >> Thanks in advance, >> ?- axel >> >> >> P.S., I do not yet have much experience with sequence analysis in BioC >> and would also be grateful for pointers to packages that could help me >> verify oligo mappings myself. > > There may be more recent examples of how to do this, but the GenomeSearching > vignette: > > http://bioconductor.org/packages/2.5/bioc/vignettes/BSgenome/inst/do c/GenomeSearching.pdf > > has a good example in section 8. You can then use the output from that > alignment with e.g. rtracklayer to visualize, or the org.Xx.eg.db package to > map to genes. I'll just add a bit to Jim's suggestions. For the 50-60mers on the Agilent array, one probably wants to map to a transcript database and NOT the genome, as many of these probes will cross exon boundaries. A program like blat or gmap (or bioconductor tools) can align the agilent probes to a trancript database such as RefSeq or Ensembl known transcripts. In the end, alignment to transcripts is what is typically sought, anyway, for gene expression arrays. Sean >> >> >> Axel Klenk >> Research Informatician >> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / >> Switzerland >> >> >> >> >> The information of this email and in any file transmitted with it is >> strictly confidential and may be legally privileged. >> It is intended solely for the addressee. If you are not the intended >> recipient, any copying, distribution or any other use of this email is >> prohibited and may be unlawful. In such case, you should please notify the >> sender immediately and destroy this email. >> The content of this email is not legally binding unless confirmed by >> letter. >> Any views expressed in this message are those of the individual sender, >> except where the message states otherwise and the sender is authorised to >> state them to be the views of the sender's company. For further information >> about Actelion please see our website at http://www.actelion.com >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >