[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Michael Lawrence lawrence.michael at gene.com
Mon Sep 11 18:58:11 CEST 2017

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.


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]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list