[BioC] Romer and symbols2indices query

[Loren Engrav]

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 at wehi.EDU.AU>
> Date: Tue, 4 May 2010 14:44:23 +1000 (EST)
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: rbioc <bioconductor at 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
> 
> 
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