[BioC] custom-made annotation packages

Marc Carlson mcarlson at fhcrc.org
Wed May 28 19:35:10 CEST 2008

Hi Sam,

Maybe you should just use SQLForge to quickly make a custom annotation 
package for yourself.  If you have ATG IDs already mapped to some kind 
of probeset ID, then this should be straightforward for you.  Nobody has 
needed to do this yet, so you will be a guinea pig making a package for 
arabidopsis, but it should work, and if it works, it should be fairly 
quick.  Have a look at the Vignette to see the more general use case and 
let me know if you have questions.

You can find the vignette here:


All you will need is some sort of mapping from whatever you want to use 
as probe labels to arabidopsis "TAIR" gene IDs (these look like: 
ATxxxxxxx).  This mapping can then be used to make a custom annotation 


Samuel Wuest wrote:
> Hi all,
> This is a conceptual question on how (if at all) to create custom-made
> annotations:
> I am using the Affymetrix plattform for Arabidopsis (ATH1), and the newest
> annotation package (AnnDbBimap objects mapping AffyIDs to e.g. GO-terms) is
> provided on the Bioconductor page, but:
> Casneuf et al (BMC Bioinformatics 2007, 8:461) have reannotated the
> Arabidopsis chip in order to get rid of cross- and nonhybridizing probes,
> and I am using the custom-made cdf-file to analyze my data. But the Affy_ID
> that naming the probesets have been replaced by gene accession numbers
> (Atg-numbers in this case) in the new cdf-file and this makes the annotation
> from Bioconductor useless to me: the keys used there are Affy_IDs.
> So obviously I have to make new mappings from gene accession numbers to e.g.
> GO-terms, but that information is available on databases.
> *My questions*: is it worth making a new annotation package for the chip, or
> could I just create my own environments that contain the mappings (if its
> only for my project)? What would be less work and still allow the main
> analyses (e.g. GO-enrichment etc)/be useful for the community?
> Also I could just try to map the gene accession numbers back to the original
> Affy_IDs and use the provided annotation package?
> And: is there an easy-to-read manual on how to create annotation packages (I
> know there are the vignettes, but I am not a bioinformatician)?
> Thanks a million for any feedback, best wishes, Sam
> 	[[alternative HTML version deleted]]
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