Thanks for the question and report Charles. I've expanded on the issue at https://github.com/waldronlab/MultiAssayExperiment/issues/274.
On Fri, Apr 17, 2020 at 5:08 AM Charles Plessy <charles.ple...@oist.jp> wrote: > Dear all, > > in the CAGEr pakcage, our main class, CAGEexp is a wrapper on the > MultiAssayExperiment class. In a typical workflow, we first create a > MultiAssayExperiment object with no experiment in, and then add the > experiments one by one as the analysis proceeds. > > As the checks in MultiAssayExperiment get tighter and tighter, I am > struggling to find the appropriate way to add experiments. Therefore, > the package is in a painful cycle of fixes followed by build failures > each time MultiAssayExperiment gets stricter. > > To solve this once for all, my questions are: > > 1) I have a MultiAssayExperiment object with no experiments in, and a > SummarizedExperiment object that I want to add as experiment. I also > made sure that `rownames(colData(object)) == colnames(value)`. How > can I add this SummarizedExperiment to the MultiAssayExperiemnt? I have > tried `object[["myExp"]] <- value` and `object <- c(object, myExp=value)` > but both of them fail. > > 2) If I want to update an experiment (for instance because I added a > new assay in a SummarizedExperiment, on which I applied a normalisation > method), what is the most appropriate way ? > > Have a nice day, > > Charles > > -- > Charles Plessy > Akano, Uruma, Okinawa, Japan > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Levi Waldron Associate Professor Department of Epidemiology and Biostatistics CUNY Graduate School of Public Health and Health Policy Institute for Implementation Science in Population Health 55 W 125th St, New York NY 10035 https://waldronlab.io [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
