[BioC] AnnotationDBI

[Marc Carlson]

Hi Tim,

If your objective is to make a custom annotation package using
AnnotationDbi, and a mapping that relates some probes to genes, then the
SQLForge vignette in the AnnotationDbi package should tell you how to
proceed.  You can find some information on that here:

http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.html

If that is not what you wanted, then please let me know.


  Marc



Tim Triche wrote:
> Sort of related-ly,
>
> Is there a good HOWTO type of document for packaging up Illumina
> annotation (CSV files/whatever) using AnnotationDbi?  I don't have any
> problem parsing the file formats, but the vignette provided seems a
> bit Affy-centric and hard for me to adapt.  I'm using R-devel and
> bioconductor-2.5 for assorted reasons.
>
> The methylation chips in particular require a little bit of chicanery,
> but that's not the problem; I'm having some issues figuring out how
> and what to put into which function so that other Bioconductor
> packages will know about the symbol, accession, etc. of the site being
> interrogated.  I wrote a bit of a hack so that 'beadarray' could
> identify control probes and M vs. U probes on Infinium, but it's ugly
> and it doesn't help after summarization into an ExpressionSetIllumina
> or NChannelSet.  I have the annotation information that I want to feed
> AnnotationDbi (as well as various masks, etc.) but I'm not sure how to
> structure it.
>
> There are a lot of (biological or sequence-related) features that can
> be used for probe masking on these arrays, of course, and I have been
> using several of them in an ad-hoc fashion (columns in a data frame
> with IlluminaIDs as rownames, excluding rows from the exprs matrix). 
> I suspect there's a better way to do this, but (for example) the
> 'methylumi' and 'lumi' packages don't help me in this endeavor.  Is
> there a customary place to store and operate upon probe masks, and is
> it separate from the annotation.db packages?  Is there a good role
> model in terms of inheriting from a mask-able eSet class?
>
> Any assistance would be appreciated -- I'm sure these problems have
> been addressed before, but I just couldn't figure out where.  Much
> obliged for anyone's time who cares to reply.
>
> --t
>
> On Fri, Sep 18, 2009 at 12:11 PM, Marc Carlson <mcarlson at fhcrc.org
> <mailto:mcarlson at fhcrc.org>> wrote:
>
>     Hi Denise,
>
>     Unfortunately, I the answer to your question is no.  The annotation
>     packages have had to undergo some pretty major schema changes in devel
>     which means that they will necessarily be incompatible with the older
>     version of AnnotationDbi that you will find in release.  So you will
>     either have to use R-devel or wait a month for R-devel to become the
>     release version if you want to use the newer packages.  In general, I
>     would recommend against mixing packages from different releases as
>     they
>     are not built or tested to work properly in this context.
>      Therefore, I
>     would also recommend against trying to install the newer AnnotationDbi
>     in the older version of R.
>
>     For your specific case, I think you should wait a month to upgrade
>     your
>     annotation packages if you can do so.  All the annotation packages are
>     being refreshed as we speak so that they can be current for the
>     upcoming
>     release of Bioconductor.  So after the new release should be an ideal
>     time to upgrade.  If you can't wait that long, then you can use
>     R-devel
>     with biocLite() to grab the latest packages.
>
>
>      Marc
>
>
>
>
>     Denise Mauldin wrote:
>     > Hey all,
>     >
>     > >From other posts on the list it appears that AnnotationDBI has
>     been updated
>     > for the most recent R-devel.  However, I'm using the 2.5
>     metadata packages
>     > to get the best updated information for my databases and the
>     hgu133a.db (and
>     > other affy) annotation packages require an AnnotationDBI that is
>     higher than
>     > 1.7.8.  Is it possible to use these packages without upgrading
>     to R-devel?
>     > I currently have R 2.9.1 installed and I don't really want to go
>     to a devel
>     > version.  Will AnnotationDBI 1.7.13 work with R 2.9.2 or is
>     there another
>     > way around this?
>     >
>     > Thanks,
>     > Denise
>     >
>     >       [[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
>     >
>     >
>
>     _______________________________________________
>     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
>
>
>
>
> -- 
> Statisticians, like artists, have a bad habit of falling in love with
> their models.
> --George Box