I should have carried the example a bit further to demonstrate the piece of code you were trying to run, geneID2GO<- readMappings(file = system.file("examples/geneid2go.map", package = "topGO")) GO2geneID<- inverseList(geneID2GO) geneNames<- names(geneID2GO) myInterestingGenes<- sample(geneNames, length(geneNames)/10) geneList<- factor(as.integer(geneNames %in% myInterestingGenes)) names(geneList)<- geneNames GOdata<- new("topGOdata", ontology = "BP", allGenes = geneList, annot = annFUN.gene2GO, gene2GO = geneID2GO) > GOdata ------------------------- topGOdata object ------------------------- Description: - Ontology: - BP 100 available genes (all genes from the array): - symbol: 068724 119608 049239 067829 106331 ... - 10 significant genes. 82 feasible genes (genes that can be used in the analysis): - symbol: 068724 119608 049239 067829 106331 ... - 9 significant genes. GO graph (nodes with at least 1 genes): - a graph with directed edges - number of nodes = 886 - number of edges = 1671 ------------------------- topGOdata object ------------------------- Valerie On 09/20/2011 08:12 AM, Valerie Obenchain wrote: > Hi Gabriel, > > The first step would be up update your version of R and BioC packages. > The current version is R-2.13 and a new release will be coming out in > late October. > > I do not get any warnings/errors in the vignette example with R-2.13, > > library(topGO) > library(ALL) > data(ALL) > data(geneList) > affyLib <- paste(annotation(ALL), "db", sep = ".") > library(package = affyLib, character.only = TRUE) > > sampleGOdata <- new("topGOdata", > description = "Simple session", ontology = "BP", > allGenes = geneList, geneSel = topDiffGenes, > nodeSize = 10, > annot = annFUN.db, affyLib = affyLib) > > > sampleGOdata > > ------------------------- topGOdata object ------------------------- > > Description: > - Simple session > > Ontology: > - BP > > 323 available genes (all genes from the array): > - symbol: 1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at ... > - score : 1 1 0.62238 0.541224 1 ... > - 50 significant genes. > > 315 feasible genes (genes that can be used in the analysis): > - symbol: 1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at ... > - score : 1 1 0.62238 0.541224 1 ... > - 50 significant genes. > > GO graph (nodes with at least 10 genes): > - a graph with directed edges > - number of nodes = 713 > - number of edges = 1424 > > ------------------------- topGOdata object ------------------------- > > > > sessionInfo() > R version 2.13.0 Patched (2011-04-14 r55448) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu95av2.db_2.5.0 org.Hs.eg.db_2.5.0 ALL_1.4.7 > [4] topGO_2.4.0 SparseM_0.89 GO.db_2.5.0 > [7] RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.14.0 > [10] Biobase_2.12.0 graph_1.30.0 > > loaded via a namespace (and not attached): > [1] grid_2.13.0 lattice_0.19-23 tools_2.13.0 > > > Valerie > > > On 09/20/2011 05:59 AM, gabriel teku wrote: >> Hi List, >> I have been trying to create a topGOdata object as follows: >> >> *GOdata<- new("topGOdata", ontology = "BP", allGenes = geneList, annot >> =annFUN.gene2GO, gene2GO = gene2GO)* >> >> where, geneList and gene2GO are as described in the topGO docs. >> >> However, I keep getting the following error: >> >> Building most specific GOs ..... >> Error in annotationFun(ontology, .Object at allGenes, ...) : >> argument "gene2GO" is missing, with no default >> >> >> I would appreciate any quick help on this issue. >> >> Below is my sessionInfo: >> >>> sessionInfo() >> R version 2.12.1 (2010-12-16) >> Platform: i386-redhat-linux-gnu (32-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] topGO_2.2.0 SparseM_0.89 GO.db_2.4.5 >> [4] RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.12.0 >> [7] Biobase_2.10.0 graph_1.28.0 biomaRt_2.6.0 >> >> loaded via a namespace (and not attached): >> [1] grid_2.12.1 lattice_0.19-13 RCurl_1.5-0 tools_2.12.1 >> [5] XML_3.2-0 >> >> >> >> >> Contact me: [image: Google Talk] gabbyteku [image: Skype] gabbyboy30 >> [image: >> MSN] gabbyteks at hotmail.com [image: Y! messenger] gabbyteku >> Signature powered by >> <http: r1.wisestamp.com="" r="" landing?u="aea70aa20c4ca423&amp;v=2.7.4&amp;t=131" 6523003272&promo="5&amp;dest=http%3A%2F%2Fwww.wisestamp.com%2Femail-install" %3futm_source%3dextension%26utm_medium%3demail%26utm_campaign%3dpromo_="" 5=""> >> >> WiseStamp<http: r1.wisestamp.com="" r="" landing?u="aea70aa20c4ca423&amp;v=2." 7.4&t="1316523003272&amp;promo=5&amp;dest=http%3A%2F%2Fwww.wisestamp.com" %2femail-install%3futm_source%3dextension%26utm_medium%3demail%26utm_c="" ampaign%3dpromo_5=""> >> >> >> [[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 > > _______________________________________________ > 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