[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Levi Waldron]

On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi,
>
> I added coercion from ExpressionSet to SummarizedExperiment in
> SummarizedExperiment 1.7.6.
>

Thank you Hervé!


> 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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