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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Laurent Gatto http://cpu.sysbiol.cam.ac.uk/ _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
