On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger < ludwig.geistlin...@bio.ifi.lmu.de> wrote:
> I guess we discussed this with Davide Risso @Bioc2017 in the > MultiAssayExperiment workshop. > > > SummarizedExperiment(mouseData) > > puts the eSet (rather counterintuitively) into `assays` of > `SummarizedExperiment`, it does not really coerce it to > SummarizedExperiment, eg. `fData` and `pData` are not accordingly > transferred to colData and rowData. > Right, I had forgotten about that - this isn't a coercion but a construction, which should be obvious from the use of a constructor function. This behavior is intuitive if you remember that SummarizedExperiment(assays, ...) is a constructor that accepts as assays any object or list of objects supporting square bracket matrix-like subsetting. Sorry for my brain hiccup there. > While I can understand that this is by design of `SummarizedExperiment`, I > really wonder whether there are use cases where somebody would like to put > an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather > would like to coerce it that way. > > Furthermore, if you would indeed like to have several `ExpressionSet`s in > a `SummarizedExperiment`, haven't you already arrived at a scenario where > use of `MultiAssayExperiment` is indicated? > I think the behavior of the constructor SummarizedExperiment() here is correct and expected, the issue here is that we're actually looking for coercion methods. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel