[Bioc-devel] Plans for multi-feature SingleCellExperiment?

Michael Lawrence |@wrence@m|ch@e| @end|ng |rom gene@com
Tue Jan 22 23:53:24 CET 2019

Hi Steve,

Pretty sure MultiAssayExperiment, containing SingleCellExperiments,
would fit the bill, but I'm not familiar with those data types.


On Tue, Jan 22, 2019 at 2:18 PM Steve Lianoglou
<mailinglist.honeypot using gmail.com> wrote:
> Comrades,
> Sorry if I'm out of the loop and have missed anything obvious.
> I was curious what the plans are in the single-cell bioconductor-verse
> to support single cell experiments that produce counts from different
> feature-spaces, such as those produced by CITE-seq / REAP-seq, for
> instance.
> In these types of experiments, I'm pretty sure we want the counts
> generated from those "features" (oligo-conjugated Antibodies, for
> instance) to be kept in a separate space than the mRNA counts. I think
> we would most  naturally want to put these in something like an
> `assay()` matrix with a different (rowwise) dimmension than the gene
> count matrix, but that can't work since all matrices in the assay()
> list need to be of the same dimensions.
> Another option might be to just add them as rows to the assay
> matrices, but keep some type of feature space meta-information akin to
> what `isSpike()` currently does;
> or add a new slot to SingleCellExperiment to hold counts from
> different feature spaces, perhaps?;
> Or rely on something like a MultiAssayExperiment?
> Or?
> Curious to learn which way you folks are leaning ...
> Thanks!
> -steve
> ps - sorry if this email came through twice, it was somehow magically
> sent from an email address I don't have access to anymore.
> --
> Steve Lianoglou
> Denali Therapeutics
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list