[Bioc-devel] SummarizedExperiment vs ExpressionSet

Peter Haverty haverty.peter at gene.com
Wed Nov 26 18:07:04 CET 2014

Hi all,

I believe there is a strong need for an object that organizes a collection
of rectangular data (matrices, etc.) with metadata on the rows and
columns.  Can SummarizedExperiment inherit from something simpler that has
a DataFrame as rowData?  (I believe GenomicRanges should inherit from
DataTable, rather than Vector, and subset as x[i,j], but maybe that's
getting a bit off topic.)  I often see people stuffing arbitrary data into
an ExpressionSet and calling one of the assays "exprs" as a work-around.



Peter M. Haverty, Ph.D.
Genentech, Inc.
phaverty at gene.com

On Wed, Nov 26, 2014 at 7:19 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:

> 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,
> Laurent
> > Thanks and best wishes
> > Wolfgang
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> --
> Laurent Gatto
> http://cpu.sysbiol.cam.ac.uk/
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