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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
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