[BioC] Romer and symbols2indices query

[Matthew Ritchie]

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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