Dear Pekka and Daniel,

Yes, the GSEA implementation in piano is one of the slowest (of the
implemented methods), however since version 1.2.0 the argument ncpus was
added and let's you run the algorithm on multiple cpus (using the R package
snowfall) thus decreasing the runtime (especially if you have access to a
computer cluster). In my trials running on 16 cpus I could save around 90%
of the time compared to the previous version.

All the best
Leif Väremo


On Fri, Jan 17, 2014 at 1:16 PM, Pekka Kohonen <pkpekka@gmail.com> wrote:

> Dear Daniel,
>
> The "piano" package does GSEA with pre-ranked genes. You can input,
> for instance, t-test statistics from limma/ebayes, fold-changes etc.
> But the method vveeeerrrryyyy sloooow compared to the Broad java
> implementation. Don't know why (maybe it would be a good idea to
> transition R to run on the jvm a la renjin, thought not sure if this
> project is still active). But you can run it.You may want to take a
> look at the options (if they are the same)
>
> Best, Pekka
>
> 2014/1/17 Daniel Schmolze <bioconductor@schmolze.com>:
> > I want to do a GSEA entirely from within R, using genes ranked by my
> > own metric. At the moment I'm saving my ranked genes to a .rnk file,
> > then calling Broad's GSEA java program, then reading the resulting
> > output back into R (all I care about are the p-values in
> > gsea_report_for_na_pos_####.xls and gsea_report_for_na_neg_####.xls).
> > Cumbersome to say the least.
> >
> > As far as I can tell, the Broad GSEA R script won't accept pre-ranked
> > genes, but maybe I'm wrong? If not, I'm interested in other options.
> > I'd like to specifically stick with the Broad GSEA algorithm if
> > possible.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

