[Bioc-devel] SummarizedExperiment vs ExpressionSet

On Wed, Nov 26, 2014 at 9:07 AM, Peter Haverty <haverty.peter at gene.com>
wrote:
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.)
Have to disagree on that. A GRanges is a vector of ranges; a table is a
list of vectors all of the same length. Different things. There was a lot
of thought invested in that. But it does subset as x[i,j], so in theory
SummarizedExperiment could be generalized to contain something with the
contract of 2D extraction.
I often see people stuffing arbitrary data into
an ExpressionSet and calling one of the assays "exprs" as a work-around.

Regards,

Pete

____________________
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

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Laurent Gatto
http://cpu.sysbiol.cam.ac.uk/

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[Bioc-devel] SummarizedExperiment vs ExpressionSet

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