Sorry, originally intended to post to BioC. Hi IainI just recently worked this out w/o errors. Use this line by line to see if this helps. Of course, in places where there are slight additions/modifications, please use the appropriate code. > library(affy) > library(topGO) > library(XXXXXXX) # annotation library, such as "hgu133plu2" - quotes are unnecessary > load("XXXXXXXXX.exprSet") > allgenes=geneNames(exprset) # for pre-R2.4 objects, use this, else the next line > allgenes=featureNames(exprset) # for post-R2.4 objects, use this, else the previous line > length(allgenes) # will tell you how many genes you have, just for verification > y2=read.table("y2.txt") # list of significant genes by your favorite stat; you can pass lists by other methods such as a SAM or multtest result as well. > y3=y2[,1] # if reading from a single col text file > geneList=factor(as.integer(allgenes %in% y3)) > names(geneList)<-allgenes > GOdata <- new("topGOdata", ontology = "MF", allGenes = geneList, affyLib = "XXXXXXX",annot=annFUN.hgu) > test.stat <- new("classicCount", testStatistic = GOFisherTest, name = "Fisher test") > resultFis <- getSigGroups(GOdata, test.stat) > l <- list(classic = score(resultFis)) > allRes2 <- GenTable(GOdata, resultFis,topNodes=150) # prints a table w. p-values > showSigOfNodes(GOdata, score(resultFis), useInfo = "all", sig.for.all=F,firstTerms=38) # based on your p-values from the test you can pick a number of nodes. My number 38 is based on a p-cutoff of 0.01 Alternate to the classic score used above you can also use alternate statistical scoring methods. > test.statel <- new("elimCount", testStatistic = GOFisherTest, name = "Fisher test",cutoff=0.05) # uses the elim method developed by Adrian Alexa > teststat2=new("classicScore",testStatistic=GOKSTest, name="KS Test") # uses a Kolmogorov-Smirnov test > teststatwt=new("weightCount",testStatistic=GOFisherTest,name="Weight Test",sigRatio="ratio") # uses a weighted test Best BALA. On Tue, Oct 7, 2008 at 11:58 AM, Iain Gallagher < iaingallagher@btopenworld.com> wrote: > ok... it was a simple error!! doh! > > instead of: > > GOdata<-new('topGOdata', ontology='BP', > allGenes=geneList, > + annot = annotFUN.gene2GO, gene2GO=test1) > > I needed > > GOdata<-new('topGOdata', ontology='BP', > allGenes=geneList, > + annot = annFUN.gene2GO, gene2GO=test1) > ie it's > annot = annFUN.gene2GO > and NOT > > annot = annotFUN.gene2GO > Great! > > Thanks again for your replies. > > Iain > --- On Tue, 7/10/08, Iain Gallagher wrote: > From: Iain Gallagher > Subject: Re: [BioC] topGO problem > To: "Adrian Alexa" > Cc: bioconductor@stat.math.ethz.ch > Date: Tuesday, 7 October, 2008, 6:52 PM > > Thanks for your replies Adrian and James. > > My data is as before. I construct the topGO data object with: > > > GOdata<-new('topGOdata', ontology='BP', > allGenes=geneList, > + annot = annotFUN.gene2GO, gene2GO=test1) > > and I get > > Building most specific GOs .....Error in .local(.Object, ...) : object > "annotFUN.gene2GO" not found > > hmm... not so good. > > > str(test1[1:10]) > List of 10 > $ ENST00000000233: chr [1:4] "GO:0007264" "GO:0015031" > "GO:0016192" "GO:0006886" > $ ENST00000000412: chr [1:4] "GO:0006810" "GO:0006898" > "GO:0008333" "GO:0015761" > $ ENST00000000442: chr [1:2] "GO:0006350" "GO:0006355" > $ ENST00000001008: chr [1:6] "GO:0006457" "GO:0006463" > "GO:0006825" "GO:0007566" ... > $ ENST00000001146: chr [1:7] "GO:0001709" "GO:0007140" > "GO:0007283" "GO:0009954" ... > $ ENST00000002165: chr [1:2] "GO:0005975" "GO:0008152" > $ ENST00000002829: chr "GO:0007275" > $ ENST00000003100: chr [1:2] "GO:0055114" "GO:0006508" > $ ENST00000003302: chr [1:3] "GO:0006511" "GO:0006512" > "GO:0008152" > $ ENST00000004531: chr [1:4] "GO:0006520" "GO:0006810" > "GO:0015807" "GO:0006865" > > looks ok > > > str(geneList) > Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ... > - attr(*, "names")= chr [1:25068] "ENST00000000233" > "ENST00000000412" "ENST00000000442" > "ENST00000001008" ... > > looks ok! > > I thought perhaps I had made a fundamental error like a spelling error some > where, but pasting in Adrians line made no difference. So I've probably > made > another error! > > Any further advice would be appreciated. > > Thanks > > Iain > > > sessionInfo() > R version 2.7.2 (2008-08-25) > i386-apple-darwin8.11.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] biomaRt_1.14.1 RCurl_0.9-4 > topGO_1.8.1 SparseM_0.78 > [5] GO.db_2.2.0 AnnotationDbi_1.2.0 RSQLite_0.6-8 > DBI_0.2-4 > [9] Biobase_2.0.0 graph_1.18.1 > > loaded via a namespace (and not attached): > [1] XML_1.96-0 cluster_1.11.11 > > > > --- On Tue, 7/10/08, Adrian Alexa wrote: > From: Adrian Alexa > Subject: Re: [BioC] topGO problem > To: iaingallagher@btopenworld.com > Date: Tuesday, 7 October, 2008, 9:36 AM > > Hi Iain, > > try this line: > > GOdata<-new('topGOdata', ontology='BP', allGenes=geneList, > annotationFun = annotFUN.gene2GO, gene2GO=test1) > > You need to specify the name of the parameters for the constructor of > a topGOdata. In your case, you forgot to match the annotFUN.gene2GO > with the annotationFun parameter. > > Regards, > Adrian > > > > > > On Mon, Oct 6, 2008 at 9:52 PM, Iain Gallagher > wrote: > > Hi > > > > I'm trying to use topGO to analyse a list of interesting genes > generated using the Affy HGU-133plus2 platform but a custom cdf. > > > > The gene universe is a list of Ensembl transcript ids. I have annotated > these with the BP GO using biomaRt > > > >> head(bio_process_go) > > go_biological_process_id ensembl_transcript_id > > 1 GO:0007264 ENST00000000233 > > 2 GO:0015031 ENST00000000233 > > 3 GO:0016192 ENST00000000233 > > 4 GO:0006886 ENST00000000233 > > 5 GO:0006810 ENST00000000412 > > 6 GO:0006898 ENST00000000412 > > > > and created a list object for feeding to topGO > > > > > > > > e.g. > > > >>test1<-unstack(bio_process_go) > >> str(test1) > > List of 13847 > > $ ENST00000000233: chr [1:4] "GO:0007264" > "GO:0015031" "GO:0016192" "GO:0006886" > > $ ENST00000000412: chr [1:4] "GO:0006810" > "GO:0006898" "GO:0008333" "GO:0015761" > > $ ENST00000000442: chr [1:2] "GO:0006350" > "GO:0006355" > > $ ENST00000001008: chr [1:6] "GO:0006457" > "GO:0006463" "GO:0006825" "GO:0007566" ... > > > > I have created the named factor which topGO should use to seperate my > interesting genes from the list. > > > > e.g. > > > >> str(geneList) > > Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ... > > - attr(*, "names")= chr [1:25068] "ENST00000000233" > "ENST00000000412" "ENST00000000442" > "ENST00000001008" ... > > > > I then create my topGO data object thus: > > > > GOdata<-new('topGOdata', ontology='BP', > allGenes=geneList, annotFUN.gene2GO, gene2GO=test1) > > > > using the annotFUN.gene2GO argument since that's the direction my > annotation goes in. > > > > However I get the following error: > > > > Building most specific GOs .....Error in .local(.Object, ...) : > > argument "annotationFun" is missing, with no default > > > > Can anyone advise on where I'm going wrong? > > > > Thanks > > > > Iain > > > >> sessionInfo() > > R version 2.7.0 (2008-04-22) > > i386-apple-darwin8.10.1 > > > > locale: > > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > > > attached base packages: > > [1] tools stats graphics grDevices utils datasets methods > base > > > > other attached packages: > > [1] topGO_1.8.1 SparseM_0.78 GO.db_2.2.0 > AnnotationDbi_1.2.0 > > [5] RSQLite_0.6-8 DBI_0.2-4 Biobase_2.0.0 > graph_1.18.1 > > [9] biomaRt_1.14.1 RCurl_0.9-4 > > > > loaded via a namespace (and not attached): > > [1] XML_1.96-0 cluster_1.11.10 > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]