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?
thanks, Francesco On Tue, Oct 24, 2017 at 3:15 AM, Kasper Daniel Hansen <kasperdanielhan...@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. > > Best, > Kasper > > On Mon, Oct 23, 2017 at 4:50 PM, Vincent Carey <st...@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 >> <franap...@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 >> > >> > _______________________________________________ >> > Bioc-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
