Hi Marc, thanks for the quick reply! So you guess it should be rather easy
to make such an annotation package?
Just to be correct with this: the ath1121501.db package uses the affy_id as
a global identifier (key values), not ATG Ids?
I'd have to create all the mappings from scratch (the GO-mappings, the KEGG
mappings, etc).

Best, Sam

2008/5/28 Marc Carlson <mcarlson@fhcrc.org>:

> 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:
>
> http://bioconductor.org/packages/2.2/bioc/html/AnnotationDbi.html
>
> 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 package.
>
>
>   Marc
>
>
>
> 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 that naming the probesets have been replaced by gene accession numbers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
>>
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>>
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>>
>
>
>

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