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.