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.resea...@gmail.com> wrote:
On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
ludwig.geistlin...@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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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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