Thanks a stack, Michael... that's crystal clear. Mental dots are joined 
and I think can take it from here. The topGO documentation was just 
really not clear.

Quin


michael watson (IAH-C) wrote:
> This code might work.
>
> In this example, my data is in a data.frame, called array2go.
>
> The column "Accn" contains the identifier for spots on the array
> The column "GO_ID" contains the GO identifier.
> The column "Category" contains the GO category.
>
> geneNames is all Accns on the array
> sigGenes is the significant set
>
> mf <- array2go[array2go$Category=="Function",]
> mygene2GO <- sapply(unique(as.vector(mf$Accn)), 
>                     function(x)
> as.character(unique(mf$GO_ID[mf$Accn==x])))
> geneNames <- unique(array2go$Accn)
> sigGenes # this comes from somewhere!
>
> geneList <- factor(as.integer(geneNames %in% sigGenes))
> names(geneList) <- geneNames
>
> GOdata <- new("topGOdata",              
>               ontology="MF",             
>               allGenes=geneList,        
>               annot=annFUN.gene2GO,    
>               gene2GO=mygene2GO)      
>
> test.stat <- new("classicCount",             
>                  testStatistic=GOFisherTest, 
>                  name="Fisher Test")         
>                  
> resultFis <- getSigGroups(GOdata, test.stat) 
>
> res <- GenTable(GOdata, classic=resultFis, topNodes=288)
> res[1:10,]
>
> -----Original Message-----
> From: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Quin Wills
> Sent: 23 October 2008 23:18
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC] How to create a GO2gene object for topGO?
>
> Hello all
>
> I have some significant Illumina v1 gene expression probes (and their 
> probe 'universe') I want to  run GO enrichment analysis on.
>
> I assume that:
> (i)  I need illumnaHumanv1.db for the GO2PROBE mappings
> (ii) I need to to create a GO2gene object for input into topGO as:
> new("topGOdata", ontology="BP", allGenes=my.probe.list, 
> annot=annFUN.GO2genes, GO2gene=my.GO2gene)
>
> I'm just not joining the mental dots dots between (i) and (ii). Or am I 
> completely missing the point? Any quick/simple guidance to get from my 
> probes to a topGOdata object would be very, very welcome - thanks!
>
> Quin **
>
> * *
>
> * *
>
> *Quin Wills*
> *DPhil candidate*
>
> * *
>
> *Department of Statistics*
>
> *University** of Oxford***
>
> *1 South Parks Road*
> *Oxford***
>
> *OX1 3TG
> United Kingdom*
>
>  
>
> *01865 285 394*
>
>
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>
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-- 

* *

* *

* *

*Quin Wills*
*DPhil candidate*

* *

*Department of Statistics*

*University** of Oxford***

*1 South Parks Road*
*Oxford***

*OX1 3TG
United Kingdom*

 

*01865 285 394*


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