Hi,
I wanted the same and this is what gsea people replied to me some months ago:


Hi,

Thank you for your interest in GSEA.

R GSEA does accept ranked list as an input.

Please note that R GSEA has not been actively maintained since 2005.

Regards,


I have not gone through the R GSEA again to check how pre-ranked lists can be accepted, but the last sentence in their message made me hold a minute and think in other possibilities.
For the moment I am still doing as you mentioned, using the rnk file with java, then getting back again from results of gsea to R.

By the way, I would like to known which metric should be best to be used for that kind of analysis when using RNA-Seq data coming from DESeq2 analysis. log2FC? p-values? Are they considered to be weighted, as GSEA pre-ranked names them?
Thanks
Regards



On 17 Jan 2014, at 00:18, Daniel Schmolze <bioconductor@schmolze.com<mailto:bioconductor@schmolze.com>> wrote:

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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