[BioC] TopGo package

Dan Tenenbaum dtenenba at fhcrc.org
Wed Mar 19 18:11:05 CET 2014 

Qian,

The idea is to provide for others everything they would need to reproduce the problem, not just code, but data.
It's understandable if you don't want to share your data though. Can you reproduce this with a small subset of your data, maybe just the first few rows? If so please attach a file containing those rows.

Also, before you call this line:

> > gt <- printGenes(day7infGOdata, whichTerms=goID, chip=" org.Dm.eg
> > ", numChar=40)

Can you confirm that day7infGOdata and goID are not NULL? Also, remove the space before org.Dm.eg, does that make any difference?

Dan


----- Original Message -----
> From: "Qian Wang" <qian.wang725 at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Bioconductor mailing list" <bioconductor at r-project.org>
> Sent: Tuesday, March 18, 2014 5:09:53 PM
> Subject: Re: [BioC] TopGo package
> 
> 
> 
> 
> 
> univ <- as.numeric( finTab $ day7 ) # fintab is a table with logical
> character(True/False) of all the genes, the significant genes from
> DEanalysis are marked with True, otherwise false; day7 is one of the
> samples
> 
> 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 )
> 
> 
> 
> 
> > goID <- allResD7inf[1,"GO:0050878"] #purpose is to check the
> > significant genes associate with the GO term 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"’
> > 
> 
> 
> 
> 
> SessionInfo()
> 
> 
> R version 3.0.2 (2013-09-25)
> 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 base
> 
> 
> other attached packages:
> [1] gplots_2.12.1 topGO_2.14.0 SparseM_1.03 GO.db_2.10.1 graph_1.40.1
> org.Dm.eg.db_2.10.1
> [7] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0
> BiocGenerics_0.8.0 matrixStats_0.8.14
> [13] cbcbSEQ_0.9.1 sva_3.8.0 mgcv_1.7-28 nlme_3.1-113
> preprocessCore_1.24.0 corpcor_1.6.6
> [19] limma_3.18.13
> 
> 
> loaded via a namespace (and not attached):
> [1] bitops_1.0-6 caTools_1.16 gdata_2.13.2 grid_3.0.2 gtools_3.3.0
> IRanges_1.20.6 KernSmooth_2.23-10
> [8] lattice_0.20-24 Matrix_1.1-2 R.methodsS3_1.6.1 stats4_3.0.2
> tools_3.0.2
> > 
> 
> 
> 
> On Tue, Mar 18, 2014 at 4:12 PM, Dan Tenenbaum < dtenenba at fhcrc.org >
> wrote:
> 
> 
> 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]]
> > > 
> > > 
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > 
> > 
> > 
> > 
> > --
> > Regards,
> > 
> > Qian Wang
> 
> 
> 
> 
> --
> Regards,
> 
> Qian Wang

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