[BioC] Romer and symbols2indices query

[Martin Morgan]

On 05/04/2010 07:57 PM, Loren Engrav wrote:
> Am back
> 
> So I have romer and GSEABase running via previous help thank you, but while
> running I explore GSEABase
> 
> And I have a lesser question for interest
> 
> In GSEABase I do
>  gmtObject <- getGMT("c2all.v2.5.symbols.gmt",
> collectionType=BroadCollection(category="c2"), geneType=SymbolIdentifier())

or maybe getBroadSets ?

>  which finishes without error
> Then
>  class(gmtObject) is GeneSetCollection
> 
> How do I convert gmtObject to a list of gene sets as required in romer when
> using

  gmtl <- geneIds(gmtObject)
  names(gmtl) <- names(gmtObject)

?

Martin

> X <- symbols2indices (ListOfGeneSets, MYsymbols)
> 
> 
> 
> 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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-- 
Martin Morgan
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