[BioC] Romer and symbols2indices query

[Loren Engrav]

Bingo, thank you
 and romer ran

These missing little tidbits can be brutal

> From: Martin Morgan <mtmorgan at fhcrc.org>
> Date: Wed, 05 May 2010 05:11:02 -0700
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: rbioc <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Romer and symbols2indices query
> 
> 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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> 
> 
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> Martin Morgan
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