[BioC] Running the GSEA algorithm

[Hooiveld, Guido]

Another useful package is "piano":
http://www.bioconductor.org/packages/release/bioc/html/piano.html

Guido


-----Original Message-----
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

Hi,

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.

-steve


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 [1] 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 [2] 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 [3] 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 [4] is arguably not 
> ideal to work with and its use is basically discouraged.
>
> - The Java version of GSEA [4] 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 
> Institute?
> Are there any other options?
>
> Thanks very much.
> Best,
>
> [1] 
> http://www.bioconductor.org/packages/release/bioc/html/GSEABase.html
> [2] http://www.bioconductor.org/packages/release/bioc/html/PGSEA.html
> [3] 
> http://www.bioconductor.org/packages/release/bioc/html/SeqGSEA.html
> [4] http://www.broadinstitute.org/gsea/downloads.jsp
>
> --
> Enrico Ferrero
> Department of Genetics
> Cambridge Systems Biology Centre
> University of Cambridge
>
>         [[alternative HTML version deleted]]
>
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--
Steve Lianoglou
Computational Biologist
Genentech

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