[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Ludwig Geistlinger Ludwig.Geistlinger at bio.ifi.lmu.de
Mon Sep 11 21:31:37 CEST 2017

Concerning 1) Why have some developers chosen to extend eSet instead of

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

> 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]]
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Dr. Ludwig Geistlinger
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de

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