Hi Sam, 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: myID1 AT1G01040 myID2 AT1G01060 myID3 AT1G01120 etc. Marc 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: > > 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > >