[BioC] TopGo package

[Dan Tenenbaum]

----- Original Message -----
> From: "Qian Wang" <qian.wang725 at gmail.com>
> To: bioconductor at r-project.org
> Sent: Tuesday, March 18, 2014 12:59:53 PM
> Subject: [BioC] TopGo package
> 
> Hi,
> 
> I am using TopGo for my gene ontology analysis of the RNA-seq data.I
> am able to get the top lists of GO terms. But I also want to print
> out the significant genes associated with a particular GO term. I am
> using printGenes.
> 
> 
> 
> day7infGOdata <- new("topGOdata",
>                   description = "Day 7 inf DE genes: DXV vs. PBS",
>                   ontology = "BP",
>                   allGenes = univ,
>                   nodeSize=10,
>                   annot = annFUN.org, mapping="org.Dm.eg")

What's the value of univ? And what is the output of

sessionInfo()

?

Dan


> resFisherD7inf <- runTest(day7infGOdata, alogorithm="classic",
> statistic="fisher")
> allResD7inf <- GenTable(day7infGOdata, classicFisher=resFisherD7inf,
> topNodes=20)
> 
> 
> > goID <- allResD7inf[1,"GO:0050878"]
> > gt <- printGenes(day7infGOdata, whichTerms=goID, chip="org.Dm.eg",
> > numChar=40)
> 
> The error message is :
> Error in (function (classes, fdef, mtable)  :
>   unable to find an inherited method for function ‘printGenes’ for
>   signature ‘"topGOdata", "NULL", "missing"’
> >
> 
> Can anybody help me?
> 
> Thanks.
> Q
> 	[[alternative HTML version deleted]]
> 
> 
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