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
