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