Very briefly, the GSEABase package has relevant utilities for gmt file
import/export and may be worth considering for these tasks.

On Tue, May 4, 2010 at 10:43 AM, Loren Engrav <engrav@u.washington.edu>wrote:

> Thank you, got it
>
> Downloading rdata objects saves reading them into an rdata object, cool
>
> But for interest, in R/GSA there is
> GSA.read.gmt(filename.gmt) to read in a .gmt file
>
> Does limma or romer have an equivalent function?
>
>
> > From: Matthew Ritchie <mritchie@wehi.EDU.AU>
> > Date: Tue, 4 May 2010 14:44:23 +1000 (EST)
> > To: Loren Engrav <engrav@u.washington.edu>
> > Cc: rbioc <bioconductor@stat.math.ethz.ch>
> > Subject: Re: [BioC] Romer and symbols2indices query
> >
> > Dear Loren,
> >
> > You can find rdata objects of the Broad's MSigDB gene sets at
> >
> > http://bioinf.wehi.edu.au/software/MSigDB/index.html
> >
> > You are right, the 'symbols' argument in the function symbols2indicies()
> > are the gene symbols corresponding to the probes from your microarray
> > data.
> >
> > For example, to use the human C2 collection, download the rdata file,
> then
> > run the following.
> >
> > load("human_c2.rdata")
> > c2 = symbols2indices(Hs.gmtl.c2, symbols)
> >
> > (this assumes 'symbols' is a vector containing the gene symbols from your
> > array data)
> >
> > Best wishes,
> >
> > Matt
> >
> >> Have done GSEA and GSA for set enrichment and am setting out to try
> romer
> >> and have probably "simple" question
> >>
> >> To get the Broad set into a list of indices there is
> >> symbols2indices(gmtl.official, symbols) but
> >>
> >> 1)how do I get the Broad set into gmtl.official? And
> >> 2)is symbols a vector of MY probe sets of interest?
> >>
> >> I checked gmane and found only one comment about romer
> >> Also checked limma reference pdf
> >>
> >> Thank you
> >
> >
> > ______________________________________________________________________
> > The information in this email is confidential and inte...{{dropped:7}}
>
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