[Bioc-devel] Biobase eSet and exprSet validation

Sean Davis sdavis2 at mail.nih.gov
Fri Feb 3 12:49:04 CET 2006

On 2/2/06 6:57 PM, "Vincent Carey 525-2265" <stvjc at channing.harvard.edu>

>>> 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.

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.


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