[BioC] Running the GSEA algorithm

Steve Lianoglou lianoglou.steve at gene.com
Mon Mar 31 23:00:01 CEST 2014


It's great to see all of these other packages popping out of the wood work.

Bioc folks: Makes me wonder if we should add a GSEA biocView to help
identify these more quickly ... I think it'd be handy.


On Mon, Mar 31, 2014 at 1:00 PM, Julian Gehring <julian.gehring at embl.de> wrote:
> Hi Enrico,
> You can also have a look at the GSRI package:
> http://bioconductor.org/packages/release/bioc/html/GSRI.html
> Best wishes
> Julian
> On 31/03/14 21:19, Enrico Ferrero 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
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Steve Lianoglou
Computational Biologist

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