[Bioc-devel] Stability of biobase eSets

Martin Morgan mtmorgan at fhcrc.org
Thu May 11 00:52:06 CEST 2006

Excellent and timely question!

1. Our plan is to never again make changes at the very end of the
development cycle. We also plan to move all our hosted experiment data
to ExpressionSet over the next few weeks -- i.e., we think this is the
future, and want to encourage feedback.

2. We have one change planned for the underlying data structure,
hopefully to make a preview by the end of this week.  Our plan is to
define a 'Versioned' class in Biobase. This class contains information
about the version of Biobase in use when an object is created. If the
object is 'serialized' (e.g., stored to disk) and retrieved at a later
date, then the version information can be consulted to check that it
is current, and can be used to update the instance to the current
definition. More details to follow shortly...

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).

4. We do not have definite plans to remove methods, but I suspect
there is room for limited housekeeping. Again, any changes at this
level will occur sooner rather than later.

5. We are also developing additional classes. These will add to,
rather than change, the existing repertoire. For instance, we are
looking at an 'EmptyMatrix' class that contains information about
dimensions and type, but not actual data. The idea is that these would
be convenient placeholders for elements missing from assayData. They
would look like matricies for many operations (is, dim, rownames, as,
[ to other EmptyMatrix, etc.) but not contain numerical

Hope that helps. Look for more information about Versioned class
shortly. Feedback most welcome!


Sean Davis <sdavis2 at mail.nih.gov> writes:

> Just a quick "developer" question--how stable are the data structures and
> methods for dealing with eSets likely to be?  I have been using eSets much
> more recently just for data handling, but I think I would probably like to
> extend them some and don't want to do that (given the availability of older,
> stable data structures) if they are going to be changing much.
> Thanks,
> Sean
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