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

[Levi Waldron]

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.plessy using 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 using 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]]