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that naming the probesets have been replaced by gene accession numbers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

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