[BioC] Agilent annotation source

[James W. MacDonald]

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/doc/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.

Best,

Jim


> 
> 
> Axel Klenk
> Research Informatician
> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
> Switzerland
> 
> 
> 
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-- 
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
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