[Bioc-devel] SummarizedExperiment vs ExpressionSet

Laurent Gatto lg390 at cam.ac.uk
Wed Nov 26 16:19:06 CET 2014

On 26 November 2014 14:59, Wolfgang Huber wrote:

> A colleague and I are designing a package for quantitative proteomics
> data, and we are debating whether to base it on the
> SummarizedExperiment or the ExpressionSet class.
> There is no immediate use for the ranges aspect of
> SummarizedExperiment, so that would have to be carried around with
> NAs, and this is a parsimony argument for using ExpressionSet
> instead. OTOH, the interface of SummarizedExperiment is cleaner, its
> code more modern and more likely to be updated, and users of the
> Bioconductor project are likely to benefit from having to deal with a
> single interface that works the same or similarly across packages,
> rather than a variety of formats; which argues that new packages
> should converge towards SummarizedExperiment(’s interface).
> Are there any pertinent insights from this group?

Instead of ExpressionSet, you could use MSnbase::MSnSet, which is
essentially an ExpressionSet for quantitative proteomics (i.e it has a
MIAPE slot, instead of MIAME for example).

Ideally, a SummarizedExperiment for proteomics would use peptide/protein
ranges, which is in the pipeline, as far as I am concerned. When that
becomes available, there should be infrastructure to coerce and MSnSet
(and/or other relevant data) into an SummarizedExperiment.

Hope this helps.

Best wishes,


> Thanks and best wishes
> Wolfgang
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Laurent Gatto

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