[BioC] pre-ranked GSEA within R?

[Pekka Kohonen]

Der Leif,

Excellent that the multi-cpu option is supported. "piano" is a very
nice package, it is easy to use and runs the commonly used methods.

Best, Pekka

2014/1/17 Leif Väremo <varemo at chalmers.se>:
> 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 at 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 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.
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at 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 at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>