[Bioc-devel] Biobase eSet and exprSet validation

[Sean Davis]

On 2/2/06 4:55 PM, "Seth Falcon" <sfalcon at fhcrc.org> wrote:

> On  2 Feb 2006, ririzarr at jhsph.edu wrote:
>> 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.

What happens with subsetting if they are not the same?  Seems like a reason
to keep the constraint.  I didn't look, sub the number of rows is also
constrained to be the same?

Sean