[BioC] GSEA for R

Steve Lianoglou lianoglou.steve at gene.com
Tue Jun 25 16:33:51 CEST 2013


On Tue, Jun 25, 2013 at 7:18 AM, January Weiner
<january.weiner at gmail.com> wrote:
> GSEA is an algorithm for testing gene set enrichment. It is
> distributed as a Java standalone program or an R script; however the R
> script is (a) crippled and (b) not straightforward to use (not really
> written "the R way").
> However, the algorithm itself seems interesting, since it (a) does not
> require arbitrary thresholds for selecting the enriched gene set and
> (b) uses a permutation approach to assess the significant changes for
> GOs, and so directly takes into account the actual variability of the
> data.
> What alternative presents itself for R?

You might try the limma::voom + limma::camera option suggested in this thread:


Or perhaps the GSVA package:


Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology

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