[BioC] GSEA using Broad genesets
zrl1974 at gmail.com
Mon Feb 8 00:25:44 CET 2010
Thank you for answering my question. Sorry I didn't make my question clearly.
In the case of "gsc <- GeneSetCollection(bcrneg_filt1,
setType=KEGGCollection())" and "Am<-incidence(gsc)", we use KEGG as
reference to create gene sets of bcrneg_filt1, then create a
My question is what if I use a download geneset database such as
"c3.all.v2.5.symbols.gmt" as reference to create gene set of
ExpressionSet bcrneg_filt1, then create a incidence matrix. Do I have
to manually do this? (I mean, identifying the genes in eset,then
correlates them in c3.all.v2.5.symbols.gmt to create gene sets) or is
there a direct command doing this?
On Sun, Feb 7, 2010 at 9:11 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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 <-
>> 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)
>  "matrix"
>  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.
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> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
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