[BioC] affy Yeast 2.0 annotation

[Vincent Carey 525-2265]

> I'm having difficulty finding a reasonable way to format the annotation
> data that Affymetrix provides (both MAGE-ML XML and a similar CSV file)
> into a BioC annotation package.
>
> I've read the AnnBuilder vignette and it seems to assume that one
> starts with a format other than what Affy provides.  I've also read
> that the RMAGE-ML package can take the Affy MAGE-ML package and format
> it for use within limma, and a few other packages, but affy (or annaffy
> or AnnBuilder) isn't listed as one of them.

RMAGEML is currently devoted to conversion from MAGE-ML archives
of experiment results to marray type data structures in R.  I understand
that this functionality will be expanded in the direction of affy
archives, but I am not sure it will address the use of MAGE-ML
for creation of platform annotation environments.

>
> Can anyone help me out as to what method would be most efficient for
> formatting this MAGE-ML file into a format acceptable for use within
> BioC as a general annotation file?  I can't find any such packages
> currently available for the Yeast 2.0 chip.

I will look at the MAGE-ML serialization and see if it is
easy to come up with something using the XML library.  But it
may well be easier to work from the CSV.

AnnBuilder would clearly be the tool of choice for this activity,
but I don't believe it can transform directly from an Affx annot CSV
to the desired set of environments.  We can improvise something
fairly simply; I recently did it for zebrafish, but the results do
not emulate exactly the structures in the other affy chip annotation
packages.

I will post some partial solutions in a few moments.  There are
various ways of getting something useful, and the path taken
will depend upon the ultimate requirements.  If we want to be sure
that something like annaffy will behave well with the target platform,
we may have more stringent requirements than if we are just interested
in doing manual lookups.