[BioC] pre-ranked GSEA within R?

Pekka Kohonen pkpekka at gmail.com
Fri Jan 17 13:16:08 CET 2014

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 at 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.
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