[BioC] Issues with BioC GO annotations and NetAffx

[Seth Falcon]

Hi Daniel,

A quick response now, hopefully I or someone else will have more time
for more detail later.

The prodcedure you described sounds reasonable and familiar in terms
of how the Bioc annotation packages are put together.  The underlying
source data (GO, Affy) change.  The GO data in particular tends to
receive many updates over short periods of time.

The Bioc annotation packages are built once for each release (every 6
months) against the version of the various source data files available
at that time.  The Bioc annotation packages are now ~5 months old so I
expect that the discrepancies you are seeing are a result of that.

You should be able to use AnnBuilder to build yourself an up-to-date
GO package and then use AnnBuilder with your new GO package to build a
fresh mouse430_2 package.  If this package has significant
discrepencies with what you are expecting, please let us know.

Best Wishes,

+ seth