[BioC] Romer and symbols2indices query

[Gordon K Smyth]

Dear Loren,

Don't forget to run

   MYsymbolsOfficial <- alias2SymbolsTable(MYsymbols,species="Hs")

(choose the appropriate species) before running

   X <- symbols2indices (ListOfGeneSets, MYsymbolOfficial)

otherwise you may miss many matches.  Matching by gene symbol is 
unreliable unless you convert everything to current official symbols.

Best wishes
Gordon



> Date: Wed, 05 May 2010 08:15:04 -0700
> From: Loren Engrav <engrav at u.washington.edu>
> To: rbioc <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Romer and symbols2indices query
> Message-ID: <C806D988.27E94%engrav at u.washington.edu>
> Content-Type: text/plain;	charset="US-ASCII"
>
>
> 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

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