[Bioc-devel] Stability of biobase eSets

Sean Davis sdavis2 at mail.nih.gov
Fri May 12 18:59:48 CEST 2006

On 5/12/06 12:36 PM, "Seth Falcon" <sfalcon at fhcrc.org> wrote:

> 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).

This is exactly the situation I had in mind, yes.  Ideally, the data would
remain the same and the class structures would be updated to as close as
possible to that in use by the current release.

> 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. :-)

I guess my more general point was that there are many (fairly complicated)
data structures that undergo change over time besides those that contain the
expression data.  When possible and when it makes sense, it might be
beneficial to think about versioning and updateClass-type ideas for them as
well.  The annotation packages might be candidates for that treatment.


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