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@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]]
> >
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> >
> >
>
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