[Bioc-devel] Biobase eSet and exprSet validation

[Vincent Carey 525-2265]

> > i agree that we should get rid of exprSet. the oligo package uses
> > the eSet exclusiveley. but we need to be very careful not lose
> > functionailty, for example, i know that exprs<- does not exist for
> > eSet. i suspect this method is used in various places
>
> I'm a bit confused about what is going on in eSet.  I see that there
> is an exprs method that is now Deprecated in favor of assayData.
>
> For using eSets in place of exprSets, I wonder if we want to revive
> that interface and make it work like this:
>
>    es <-  ## an eSet instance
>
>    exprs(es) - If es at assayData has length 1, return the first element,
>    otherwise, error.  Same for replacement.
>
>    exprs(es, n) - Return the n-th element of assayData.  This won't
>    work if assayData is an environment unless we store some additional
>    info that defines the order.
>
> Also, I'm confused about the constraint on the number of columns in
> the expression matrices stored in assayData.  Can they be different?
> My glance at the validEset function gives me the feeling that they
> cannot, but then I'm confused about why ncol should report ncol for
> each if they are constrained to be the same.

we need use cases.  i don't think anyone ever tried to work with
multicolor arrays in this context.  i wrote the initial validity
conditions i think because no one had any objections to that constraint
(common dimensions)

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.