[BioC] Romer and symbols2indices query

[Loren Engrav]

Ah yes, cool, I will use it

I have now run GSEA, R/GSA and limma/romer
I suppose could try PGSEA and GSEAlm

But maybe the first 3 are enough
Maybe time to quit fiddling



> From: Vincent Carey <stvjc at channing.harvard.edu>
> Date: Tue, 4 May 2010 11:40:39 -0400
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: rbioc <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Romer and symbols2indices query
> 
> 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 at 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 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
>>> 
>>> 
>>> ______________________________________________________________________
>>> The information in this email is confidential and inte...{{dropped:7}}
>> 
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