[BioC] GSEA using Broad genesets

[zrl]

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?



Thanks.

Qiudao