[BioC] TopGo package

[Dan Tenenbaum]

Hi Qian,

Please keep the Bioconductor list in the loop (hit Reply All) that way we can all teach and learn. 

For best results, you need to provide all the code necessary to reproduce the problem. You haven't done that below, because we still don't know what finTab and day7 are. 

Also, please run the function 
sessionInfo()

...after you get your error, and then paste its output into your email. This tells us about your operating system, R version, and version of packages loaded, which can help us figure out what the problem is. This is what my sessionInfo() looks like:

> sessionInfo()
R Under development (unstable) (2013-10-12 r64048)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] topGO_2.15.2          SparseM_1.03          GO.db_2.10.1         
 [4] RSQLite_0.11.4        DBI_0.2-7             AnnotationDbi_1.25.15
 [7] GenomeInfoDb_0.99.19  Biobase_2.23.6        BiocGenerics_0.9.3   
[10] graph_1.41.3         

loaded via a namespace (and not attached):
[1] grid_3.1.0      IRanges_1.21.34 lattice_0.20-27 stats4_3.1.0   
[5] tools_3.1.0    

Thanks,
Dan


----- Original Message -----
> From: "Qian Wang" <qian.wang725 at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Sent: Tuesday, March 18, 2014 4:06:17 PM
> Subject: Re: [BioC] TopGo package
> 
> 
> 
> 
> univ <- as.numeric( finTab $ day7 )
> 
> univ <- as.factor( univ )
> 
> names( univ ) <- finTab $ gene_id
> 
> head( univ )
> 
> 
> 
> 
> # make topGOdata object
> 
> day7GOdata <- new( "topGOdata" ,
> 
> description = "Day 7 DE genes: Wt vs. Mut" ,
> 
> ontology = "BP" ,
> 
> allGenes = univ ,
> 
> nodeSize = 10 ,
> 
> annot = annFUN.org , mapping = " org.Dm.eg " )
> 
> resFisher <- runTest( day7GOdata , alogorithm = "classic" , statistic
> = "fisher" )
> 
> allRes <- GenTable( day7GOdata , classicFisher = resFisher , topNodes
> = 20 )
> 
> par( fig =c( 0 , 1 , 0 , 1 ), mar =c( 3 , 5 , 2 , 0.5 ))
> 
> 
> 
> 
> this is the GO analysis Code. Not sure whether answers your
> questions. I am new to R.
> 
> 
> Thanks.
> Q
> 
> 
> 
> On Tue, Mar 18, 2014 at 3:30 PM, Dan Tenenbaum < dtenenba at fhcrc.org >
> wrote:
> 
> 
> 
> 
> 
> ----- 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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> 
> 
> 
> 
> --
> Regards,
> 
> Qian Wang