An ExpressionSet is an eSet that is guaranteed to have an "exprs" assay. That makes no sense for example for methylation where we have (say) Green/Red assays or Meth/Unmeth assays (or transformations of these).
Best, Kasper On Mon, Sep 11, 2017 at 3:31 PM, Ludwig Geistlinger < ludwig.geistlin...@bio.ifi.lmu.de> wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
