[BioC] Romer and symbols2indices query

[Loren Engrav]

Thank you very much, this is interesting

I did as you suggest and 7 of 1842 symbols were "incorrect"

I will fix and rerun

Thank you again, am grateful



> From: Gordon K Smyth <smyth at wehi.EDU.AU>
> Date: Fri, 7 May 2010 10:35:55 +1000 (AUS Eastern Standard Time)
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: Yifang Hu <hu at wehi.edu.au>, rbioc <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Romer and symbols2indices query
> 
> 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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