[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Levi Waldron]

On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:

> I guess we discussed this with Davide Risso @Bioc2017 in the
> MultiAssayExperiment workshop.
>
> > SummarizedExperiment(mouseData)
>
> puts the eSet (rather counterintuitively) into `assays` of
> `SummarizedExperiment`, it does not really coerce it to
> SummarizedExperiment, eg. `fData` and `pData` are not accordingly
> transferred to colData and rowData.
>

Right, I had forgotten about that - this isn't a coercion but a
construction, which should be obvious from the use of a constructor
function. This behavior is intuitive if you remember that
SummarizedExperiment(assays, ...) is a constructor that accepts as assays
any object or list of objects supporting square bracket matrix-like
subsetting. Sorry for my brain hiccup there.


> While I can understand that this is by design of `SummarizedExperiment`, I
> really wonder whether there are use cases where somebody would like to put
> an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
> would like to coerce it that way.
>
> Furthermore, if you would indeed like to have several `ExpressionSet`s in
> a `SummarizedExperiment`, haven't you already arrived at a scenario where
> use of `MultiAssayExperiment` is indicated?
>

I think the behavior of the constructor SummarizedExperiment() here is
correct and expected, the issue here is that we're actually looking for
coercion methods.

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