[Bioc-devel] Modeling (statistic, p-value) pairs in MultiAssayExperiment
franapoli at gmail.com
Tue Oct 24 12:14:05 CEST 2017
I'm converting gene expression profiles to "pathway expression
profiles" (https://doi.org/10.1093/bioinformatics/btv536), so for each
pathway I have an enrichment score and a p-value. I guess it would be
like modeling gene expression data where limma-like preprocessing was
performed, so you have a fold change - p-value pair for each gene.
Isn't there a data model for that?
On Tue, Oct 24, 2017 at 3:15 AM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> Are you discussing statistics of the same dimension as the data (unusual) or
> summary statistics? We should think about a MAE version of summary
> statistics, but that is not captured in current representation I would say.
> On Mon, Oct 23, 2017 at 4:50 PM, Vincent Carey <stvjc at channing.harvard.edu>
>> no answers yet? would it work to put your matrices as separate assays in
>> 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>
>> > 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
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> [[alternative HTML version deleted]]
>> Bioc-devel at r-project.org mailing list
More information about the Bioc-devel