[BioC] custom-made annotation packages
mcarlson at fhcrc.org
Wed May 28 20:27:57 CEST 2008
SQLForge will make almost all of the mappings (GO, KEGG, etc) for you.
All you need to provide is a single mapping from whatever probe type of
IDs you want to use mapped onto the appropriate TAIR IDs. Then you
should only have to download two packages and call a single function to
make the package (read the SQLForge vignette for details). The
ath1121501.db package that you are referring to was made using this same
function, only its mapping was a file from Affymetrix. As long as you
know what probe goes with what TAIR ID, we should be able to make a
package from that.
So for example you just need to have a bunch of IDs (these can be
anything you want) that are mapped to TAIR IDs (which look like:
ATxxxxxxx) then you need a tab separated file that looks something like:
Samuel Wuest wrote:
> 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 at fhcrc.org <mailto:mcarlson at 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:
> 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.
> Samuel Wuest wrote:
> Hi all,
> This is a conceptual question on how (if at all) to create
> 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
> (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]]
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> <mailto:Bioconductor at stat.math.ethz.ch>
> Search the archives:
More information about the Bioconductor