[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Kasper Daniel Hansen]

An ExpressionSet is an eSet that is guaranteed to have an "exprs" assay.
That makes no sense for example for methylation where we have (say)
Green/Red assays or Meth/Unmeth assays (or transformations of these).

Best,
Kasper

On Mon, Sep 11, 2017 at 3:31 PM, Ludwig Geistlinger <
Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:

> Concerning 1) Why have some developers chosen to extend eSet instead of
> ExpressionSet:
>
> As far as I understand it, ExpressionSet was thought to exclusively
> represent a microarray experiment (MIAME = Minimum Information About a
> Microarray Experiment).
>
> Thus, back in the days when more and more people started using RNA-seq and
> there was no SummarizedExperiment, developers extended eSet with e.g.
> assayData slots called `counts` instead of `exprs` to represent RNA-seq
> data.
>
>
> > 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?
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> --
> Dr. Ludwig Geistlinger
> eMail: Ludwig.Geistlinger at bio.ifi.lmu.de
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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