[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Concerning 1) Why have some developers chosen to extend eSet instead of
ExpressionSet:

As far as I understand it, ExpressionSet was thought to exclusively
represent a microarray experiment (MIAME = Minimum Information About a
Microarray Experiment).

Thus, back in the days when more and more people started using RNA-seq and
there was no SummarizedExperiment, developers extended eSet with e.g.
assayData slots called `counts` instead of `exprs` to represent RNA-seq
data.

On Mon, Sep 11, 2017 at 2:02 PM, Herv?? Pag??s <hpages at fredhutch.org>
wrote:

Hi,

I added coercion from ExpressionSet to SummarizedExperiment in
SummarizedExperiment 1.7.6.

Thank you Herv??!

The current behavior of the SummarizedExperiment() constructor
when called on a ExpressionSet object doesn't make much sense to
me. I'd rather have it consistent with what the coercion does.
Will fix it.

Thank you, again.

A couple more questions while I'm at it, that may expose the limitations
in
my understanding of inheritance and project history... 1) Why have some
developers chosen to extend eSet instead of ExpressionSet (definition
<https://github.com/Bioconductor/Biobase/blob/

536f137165ca08b3be22819e51e055b3e7afe86d/R/DataClasses.R#L166>),

and 2) why are these coercion methods developed for ExpressionSet rather
than eSet? Wouldn't an eSet coercion method be preferable because it

would

cover ExpressionSet as well as all the classes that extend eSet?

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--
Dr. Ludwig Geistlinger
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de