[BioC] Running the GSEA algorithm
guido.hooiveld at wur.nl
Mon Mar 31 21:56:39 CEST 2014
Another useful package is "piano":
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Steve Lianoglou
Sent: Monday, March 31, 2014 21:23
To: Enrico Ferrero
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Running the GSEA algorithm
For more GSEA options, check out the camera, roast, and romer function in limma (2/3 of those are also in edgeR).
The respective vignettes have more info.
On Mon, Mar 31, 2014 at 12:19 PM, Enrico Ferrero <enricoferrero86 at gmail.com> wrote:
> Hi everyone,
> I would like to include GSEA into my R analytical pipelines, but I'm
> struggling to understand what's the best way to implement it. The
> following information might be incomplete or even wrong, but here is
> what I understood so far:
> - The GSEABase package  provides an excellent infrastructure for
> dealing with gene sets and gene sets collections but, as far as I
> understand, doesn't provide a way to run the GSEA algorithm.
> - The PGSEA package  provides a minimal, and perhaps simplistic,
> interface to GSEA. It does run the analysis but only outputs a matrix
> with what I understand is a score (possibly the NES?) and nothing else.
> - The SeqGSEA package  allows to run the GSEA algorithm and also
> produces some excellent plots of gene sets enrichment. However, it
> works with with RNA-seq count data and I don't see how it could be
> adapted to microarray data.
> - The GSEA-P-R package from the Broad Institute  is arguably not
> ideal to work with and its use is basically discouraged.
> - The Java version of GSEA  is probably my best bet at the moment,
> as it allows command-line usage and provides a complete output for the analysis.
> So, am I missing something here?
> Is there an established way to run the GSEA algorithm from R using
> Bioconductor packages that also works for non-NGS data?
> If not, would anybody recommend the GSEA-P-R package from the Broad
> Are there any other options?
> Thanks very much.
>  http://www.bioconductor.org/packages/release/bioc/html/PGSEA.html
>  http://www.broadinstitute.org/gsea/downloads.jsp
> Enrico Ferrero
> Department of Genetics
> Cambridge Systems Biology Centre
> University of Cambridge
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> Bioconductor at r-project.org
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