[BioC] annotation package for chicken affyprobes

[James W. MacDonald]

Hi Lina,

Lina Hultin-Rosenberg wrote:
> Dear list!
> 
> I am working on some affymetrix data on chicken and am using R for analysis
> of the data. I would like to add annotation data and as far as I can see
> there is no annotation package for chicken at bioconductor. When reading the
> vignette for AnnBuilder I got the impression that packages can only be built
> for organisms human, rat and mouse so far. It also said: See section Extend
> AnnBuilder if you have an organism other than the three species. But the
> Extend AnnBuilder section is empty. My question is if I can build an
> annotation package for chicken using AnnBuilder and how I would do that?

I am sure Nianhua will respond with some ideas of how to build an 
annotation package, but if this isn't possible (or is very difficult), 
you might consider using the biomaRt package to annotate your probesets. 
You can get quite a bit of annotation this way, and you can even use 
your affy probeset IDs to annotate, rather than having to convert to 
Entrez Gene or UniGene IDs first.

If your goal is to output a list of the top probesets along with 
annotation, you might look at the affycoretools package, which has some 
wrapper functions intended to simplify the output of HTML tables using a 
set of probe IDs (or output from limma). There will also be a vignette 
that explains some of these functions in more detail as soon as I get it 
to quit erroring out on the BioC build servers ;-D.

Note that these functions are in the devel version of affycoretools, so 
you if you want to use them, you will need the devel version of R as well.

HTH,

Jim


> 
> Thank you!
> 
> Best regards,
> 
> Lina Hultin Rosenberg
> 
> ________________________________
> Lina Hultin Rosenberg
> Msc Molecular Biotechnology
> Evolutionary Biology Department
> Uppsala University
> Norbyvägen 18
> 752 36 Uppsala
> Phone: +46-18-4716444
> Email: lina.hultin.rosenberg at ebc.uu.se
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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