[Bioc-devel] Biobase eSet and exprSet validation

[Seth Falcon]

On  3 Feb 2006, sdavis2 at mail.nih.gov wrote:
>> Vince wrote:
>> eSet means (perhaps) "everything" set, and there is no
>> justification to interpret a single assayData matrix as expression.
>> so making the exprs method look for something named "exprs" makes
>> some sense.

ok, I was missing some concepts and am in agreement that we don't want
to force an eSet with a length one assayData slot to be an exprSet
equivalent.

> Going with the MIAME thought process, it makes sense to have an
> exprs() matrix and an se.exprs() matrix that are treated as
> "special" (the "derived measurement values" and the "reliability
> indicator" in the MIAME 1.1 draft).  I think having some standard
> here is important for general development purposes (other packages
> need to know where to get data for processing).  Then, the other
> matrices in assayData are simply "raw data" and could be obtained
> using standard list accessors.

So it sounds like the original implementation in which special names
are recognized for identifying elements of the assayData is sensible?
If we put this back in, I propose more verbose names:

expressionValues 
expressionStandardErrors

The method names should not change: exprs() and se.exprs(),
respectively.

One thing I'm wondering, however, is whether these deserve their own
slots?  The magic list/env element names make me nervous --- going
down that road, we could start putting more and more special names in
the list/env and it really starts to look like an object without any
real definition.

+ seth