[BioC] GSEA using Broad genesets

[zrl]

Hi Martin,

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
incidence.

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?
Thanks.






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 <-
>> 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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>
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