[BioC] Can any one please help me regadrding Illumina humanv3.microarray

[Steve Lianoglou]

Hi,

On Mon, Nov 8, 2010 at 10:44 AM, Pradeep Battula <prabat at utu.fi> wrote:
> Dear All,
>
> I want to write a function that performs hypergeometric test for over representation against GO and KEGG, for the available example of data of
> background.Datat: Entrez identifiers of all probes present on Illumina human HT12 v3. microarray
> DEgenes.Data: Differentially expressed genes in a real study carried out on Illumina HT12 v3. microarray
>
> But, the relevant documentation provided in "GOstats" and "topGO" are explained using a microarray data set  from a clinical trial in acute lymphoblastic leukemia (ALL).
>
> Now I want to know, can I apply the same documentation to my available data or there any minor changes I have to make.

If both your background.Data and DEgenes.Data are simply vectors of
entrez id's, then this is pretty straightforward. With GOstats, you
can do:

R>   params <- new("GOHyperGParams", geneIds=DEgenes.data,
                universeGeneIds=background.Data, annotation='org.Hs.eg.db',
                ontology='BP', ...)
R> go.bp <- hyperGTest(params)

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact