[Bioc-devel] Biobase eSet and exprSet validation

[Seth Falcon]

On  2 Feb 2006, stvjc at channing.harvard.edu wrote:
>> Now might also be a good time to replace any use of the deprecated
>> eset data with the new sample.eSet and sample.exprSet data sets.
>
> how about converting all serialized exprSets to eSets?  there is an
> "as" operator to help with this in Biobase...
>
> should we try to eliminate all reliance on exprSets?  it can only be
> confusing to newcomers that there are two basic containers
> doing the same thing.

I think it would be beneficial to solidify and simplify the basic
container(s).  

A first step, IMO, is to update the vignette that describes eSets.
The vignette should probably renamed and the provisional comments
removed. 

A second step would be to updte the Biobase vignette to reflect that
eSets are the main show in town.

If there is consensus that eSets are "ready", then at the same time as
the above two steps, package maintainers could start to convert
vignettes and examples to using eSets and ensure that all functions
know how to deal with eSets.

But for functions that currently know how to process exprSets, what
should the behavior be when processing an eSet which may have multiple
expression matrices?  Should the function check that there is only
one?  Should the function gain an arg that specifies which matrix to
operate on?  Should functions be changed so that they always return a
list of results and always do operations on all matrices present?

I think we need to hash out some answers and examples to the above
before we can start calling as(foo, "eSet").  Am I making a mountain
out of a mole hill?

Best Wishes,

+ seth