[BioC] Agilent annotation source

James W. MacDonald jmacdon at med.umich.edu
Thu Feb 4 15:29:42 CET 2010

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:


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.



> 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.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 

More information about the Bioconductor mailing list