[Bioc-devel] SummarizedExperiment vs ExpressionSet

Wolfgang Huber whuber at embl.de
Wed Nov 26 15:59:55 CET 2014

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?

Thanks and best wishes

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