[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Hervé Pagès]

Hi,

I added coercion from ExpressionSet to SummarizedExperiment in
SummarizedExperiment 1.7.6.

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.

Cheers,
H.

On 09/11/2017 09:58 AM, Michael Lawrence wrote:
> It's probably good keeping coercion and construction distinct,
> although we have violated that recently with GRanges(). It now
> attempts to coerce its first argument to a GRanges. Don't want to
> derail the discussion, but it's another data point.
>
> Michael
>
> On Mon, Sep 11, 2017 at 9:26 AM, Levi Waldron
> <lwaldron.research at gmail.com> wrote:
>> 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.
>>
>>          [[alternative HTML version deleted]]
>>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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