[BioC] GSEA for R

January Weiner january.weiner at gmail.com
Tue Jun 25 16:39:20 CEST 2013

Thank you all for your answers. The limma functions are great and are
exactly what I need.

Kind regards,


On 25 June 2013 16:33, Steve Lianoglou <lianoglou.steve at gene.com> wrote:
> 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

-------- January Weiner --------------------------------------

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