[Bioc-devel] Biobase eSet and exprSet validation
Vincent Carey 525-2265
stvjc at channing.harvard.edu
Fri Feb 3 00:57:01 CET 2006
> > 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
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.
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