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

Levi Waldron |w@|dron@re@e@rch @end|ng |rom gm@||@com
Sun Apr 19 20:24:28 CEST 2020

Thanks for the question and report Charles. I've expanded on the issue at

On Fri, Apr 17, 2020 at 5:08 AM Charles Plessy <charles.plessy using oist.jp>

> 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
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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


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