[BioC] GSEA using Broad genesets

[Martin Morgan]

On 02/06/2010 04:05 PM, zrl wrote:
> Dear list,
> 
> I have a question regarding using broad gene sets for GSEA anlaysis.
> 
> As we know, we have "gsc <- GeneSetCollection(bcrneg_filt1,
> setType=KEGGCollection())" and "Am<-incidence(gsc)" to generate
> incidence matrix for further anlaysis.
> 
> I have learned to get the geneset file from Broad such as: "c3gsc2 <-
> getGmt("/path/to/c3.all.v2.5.symbols.gmt",
> collectionType=BroadCollection(category="c3"),
> geneIdType=SymbolIdentifier())"
> 
> My question is how to use c3gsc2 and bcneg_filt1 to create a new
> incidence matrix ? Do I have to manually do this? or there is a
> command which can do this?

Hi Quidao

bcneg_filt1 is a subset of an ExpressionSet, and is just another source
for creating a gene set collection. Here you're using
c3.all.v2.5.symbols.gmt as a source for your gene set collection. The
incidence matrix is

> m <- incidence(c3gsc2)
> class(m)
[1] "matrix"
> dim(m)
[1]   837 15718
> m[1:5, 1:5]
                        DLC1 FLJ39378 PTGS1 RORC VPRBP
RGAGGAARY_V$PU1_Q6         1        1     1    1     1
KRCTCNNNNMANAGC_UNKNOWN    0        0     0    0     0
AAAYWAACM_V$HFH4_01        0        0     0    0     0
YYCATTCAWW_UNKNOWN         0        0     0    0     0
CYTAGCAAY_UNKNOWN          0        0     0    0     0

with rows as set names and columns as symbols.

Martin

> 
> 
> 
> Thanks.
> 
> Qiudao
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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