[Bioc-devel] Modeling (statistic, p-value) pairs in MultiAssayExperiment

[Levi Waldron]

Just realized my answer yesterday went to Francesco and not the list:

Since it sounds like you have two matrices of the same dimensions, why not
represent these as two assays in a SummarizedExperiment?  E.g.:

> statvals <- matrix(rnorm(100), ncol=5)
> pvals <- pnorm(statvals)
> library(SummarizedExperiment)
> se <- SummarizedExperiment(list(statvals = statvals, pvals = pvals))
> se
class: SummarizedExperiment
dim: 20 5
metadata(0):
assays(2): statvals pvals
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):
>

If you then have more than one of these, with different dimensions, then
MultiAssayExperiment would be of use to you.

(PS: this question is probably better suited for support.bioconductor.org)



On Oct 23, 2017 4:50 PM, "Vincent Carey" <stvjc at channing.harvard.edu> wrote:

> no answers yet?  would it work to put your matrices as separate assays in a
> SummarizedExperiment?
> as long as they are conformant in dimensions and dimnames I think that
> would work.  That
> SummarizedExperiment would then work well in an MAE.
>
> On Mon, Oct 23, 2017 at 1:00 PM, Francesco Napolitano <franapoli at gmail.com
> >
> wrote:
>
> > Hi,
> >
> > I'm trying to build a MultiAssayExperiment. However, in my case each
> > assay should ideally include two matrices: one with a statistic and
> > another one with the corresponding p-value. I'm currently managing
> > each of them simply as a list of two matrices, but assay class expects
> > table-like data. I must also be able to quickly extract entire rows or
> > columns from each matrix.
> >
> > Is there a suitable way to model this into a MultiAssayExperiment?
> >
> > Thank you,
> > Francesco
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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