[BioC] GSEA for R

[Steve Lianoglou]

Hi,

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:

https://stat.ethz.ch/pipermail/bioconductor/2012-May/045420.html

Or perhaps the GSVA package:

http://bioconductor.org/packages/release/bioc/html/GSVA.html

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech