Concerning 1) Why have some developers chosen to extend eSet instead of ExpressionSet:
As far as I understand it, ExpressionSet was thought to exclusively represent a microarray experiment (MIAME = Minimum Information About a Microarray Experiment). Thus, back in the days when more and more people started using RNA-seq and there was no SummarizedExperiment, developers extended eSet with e.g. assayData slots called `counts` instead of `exprs` to represent RNA-seq data. > On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès <hpa...@fredhutch.org> > wrote: > >> Hi, >> >> I added coercion from ExpressionSet to SummarizedExperiment in >> SummarizedExperiment 1.7.6. >> > > Thank you Hervé! > > >> The current behavior of the SummarizedExperiment() constructor >> when called on a ExpressionSet object doesn't make much sense to >> me. I'd rather have it consistent with what the coercion does. >> Will fix it. >> > > Thank you, again. > > A couple more questions while I'm at it, that may expose the limitations > in > my understanding of inheritance and project history... 1) Why have some > developers chosen to extend eSet instead of ExpressionSet (definition > <https://github.com/Bioconductor/Biobase/blob/536f137165ca08b3be22819e51e055b3e7afe86d/R/DataClasses.R#L166>), > and 2) why are these coercion methods developed for ExpressionSet rather > than eSet? Wouldn't an eSet coercion method be preferable because it would > cover ExpressionSet as well as all the classes that extend eSet? > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Dr. Ludwig Geistlinger eMail: ludwig.geistlin...@bio.ifi.lmu.de _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel