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

Levi Waldron lwaldron.research at gmail.com
Tue Oct 24 14:45:05 CEST 2017

On Oct 24, 2017 6:14 AM, "Francesco Napolitano" <franapoli at gmail.com> wrote:

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?

Nice paper, thanks for the link! Could you explain the problem a little
more using the terminology of your paper? I see your enrichment values
matrix (fig 1c *ES*ij) of pathways x cell lines, and imagine additional
associated matrices of p-values and ranks, but where do assays with
different rows come in?

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