[BioC] Romer and symbols2indices query

[Gordon K Smyth]

Dear Loren,

I don't understand why you would want to read in a gmt file from the Broad 
Institute rather than use the curated rdata files that we provide for use 
with romer.  The raw gmt files contain a mix of gene symbols of different 
species and a mix of official and non-official symbols.  So one can't 
expect to match the symbols you get from a raw gmt file to your own data 
with any reliability.  To construct the rdata files, we have carefully 
converted all gene aliases to official symbols and have mapped mouse to 
human and human to mouse orthologs.

This is the reason why we don't provide a read.gmt() function in limma, or 
a pre-made pipeline from the GSEABase read functions.  We don't want you 
to get unreliable results simply because the gene symbols haven't been 
curated.

Best wishes
Gordon

> Date: Tue, 04 May 2010 07:43:46 -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: <C80580B2.27D83%engrav at u.washington.edu>
> Content-Type: text/plain;	charset="US-ASCII"
>
> 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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