Message-ID: <CAOUXvx6jKZd-G_2v1PdA4n=WZr=5n2==HJtXfCbhgkQsSeZw1g@mail.gmail.com>
Date: 2017-10-24T12:45:05Z
From: Levi Waldron
Subject: [Bioc-devel] Modeling (statistic, p-value) pairs in MultiAssayExperiment
In-Reply-To: <CAGvyyhuRWGuO8k4Mq+sNmsK=Dk1gHE-nt_tr9WBGzQH8P1BsKw@mail.gmail.com>
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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