[Bioc-devel] Stability of biobase eSets

[Seth Falcon]

Sean Davis <sdavis2 at mail.nih.gov> writes:
>> 3. We plan to introduce a new method, updateClass, that can be
>> used to update instances, either to their current version or to a
>> different representation (e.g., from exprSet to ExpressionSet, but
>> allowing more flexibility than 'setAs' methods might).
>
> Sounds good.  I would think that the annotation packages might benefit 
> from this as well, as often peoples' analyses were based on a particular 
> set of annotations and switching would result in different results.

I'm not sure what you have in mind here.  The updateClass idea allows
for a way of dealing with the following situation: you have saved an
instance X of a given class FOO and later updated the class definition
for FOO.  When you load X, updateClass will provide for a means to
attempt to update the data contained in the instance to the new class
definition structure (imagine a case where a slot was renamed as a
simple example).

Certainly annotation data changes over time and results will change
with it, but I don't think there is much we can/want to do about
that.  If you want the same results, use the same versions of the
annotation data.  If I've misunderstood, please feel free to explain
further.  I don't want to discourage suggestions or ways we can make
the software more useful. :-)

+ seth