[Bioc-devel] How to add an experiment to an empty MultiAssayExperiment file ?

Charles Plessy ch@r|e@@p|e@@y @end|ng |rom o|@t@jp
Fri Apr 17 05:07:36 CEST 2020

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 Plessy
Akano, Uruma, Okinawa, Japan

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