As Sean noted, exporting the data from GenomeStudio with an up-to-date 450k
manifest is a perfectly reasonable way to annotate your results if you are
not pumping them directly into a package like GeneAnswers (or similar
packages that expect deeper integration).

If someone wants to help beta test a 450k annotation package, I'm not
opposed to making it available, with the understanding that it is not yet
Bioconductor release quality.  The idea would be to tie up any loose ends
related to documentation of certain new mapping fields, and thus get the
documentation and integration up to the expectations of BioC users.  The
core Bioconductor developers have been extremely generous with their time in
helping me get up to speed and I'd like to hear what they think about such
an idea before proceeding.

Depending on how you process, export, and annotate the results of a given
27k or 450k experiment, it's possible to end up with diverging results.
 This bothered me, so I wrote a package to decouple the preprocessing from
GenomeStudio and focus on IDAT files (pretty much the same way that CEL
files are standard for Affymetrix output).  The codebase for processing
27k/450k chips from raw IDAT files is available from GitHub. I could post
updated annotations there as well:  https://github.com/ttriche/methylumIDAT

Please note that the above codebase is not up to Bioconductor standards yet.
 In particular, all but the most critical user-facing functions are
undocumented, save for comments.  Once the package gets more documentation
and testing, I hope to merge it into methylumi, and with any luck that
should happen before the next major release.  Some of the generic functions
should probably be merged sooner, so I'll try sending a pull request or some
patches and get those into the development version of methylumi this week.

--t


On Tue, Feb 15, 2011 at 3:48 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Tue, Feb 15, 2011 at 6:42 AM, Dario Greco <dario.greco@helsinki.fi
> >wrote:
>
> > Dear friends.
> > i am starting the analysis of a set of Infinium Human Methylation 450k
> > beadchips and I would like to run the analysis with lumi/methylumi.
> > i have seen track in mailinlist of a possible update back during last
> fall.
> > what is the situation at the moment? apparently, there is not yet an
> > annotation package for the infinium 450k.
> >
>
> Hi, Dario.  There is not one publicly available right now, no.  That said,
> if you do your genomestudio export with all the annotation columns, those
> are loaded by methylumi, so the annotation comes along for the ride by
> default.  We hope to have an annotation package in place for the next
> release.
>
> Sean
>
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