Hi Heike, I just looked at your data and the problem seems to be with geneList. More exactly, the geneList and go_list don't match at all. The gene identifiers in indexing the go_list are totally different from the gene identifiers found in the geneList! library(topGO) ## load the data load("myGOdata.RData") ## the list of all gene ID's geneNames <- names(go_list) str(geneNames) length(intersect(names(geneList), geneNames)) ## this is 0! I think you mixed the annotations or the process of building the list of interesting genes. There needs to be an overlap between the identifiers in the GO-to-gene mapping and the list of interesting genes. Bellow I generated a random set of interesting genes just to test if one can build the topGOdata object based on the go_list: ## generate a random list of interesting genes ## select (or define) the list of interesting genes myInterestedGenes <- sample(geneNames, 100) ## make a indicator vector showing which genes are interesting myGeneList <- factor(as.integer(geneNames %in% myInterestedGenes)) names(myGeneList) <- geneNames str(myGeneList) sum(as.integer(myGeneList) == 2) ## should be 100 ## build the topGOdata class ## there are three annotation functions available: ## 1. annFUN.db -- used for bioconductor annotation chips ## 2. annFUN.gene2GO -- used when you have mappings from each gene to GOs ## 3. annFUN.GO2genes -- used when you have mappings from each GO to genes ## GOdata <- new("topGOdata", ontology = "MF", allGenes = myGeneList, annot = annFUN.gene2GO, ## the new annotation function gene2GO = go_list) ## the gene ID to GO dataset ## display the GOdata object GOdata ------------------------- topGOdata object ------------------------- Description: - Ontology: - MF 20623 available genes (all genes from the array): - symbol: TM00000001 TM00000002 TM00000003 TM00000004 TM00000005 ... - 100 significant genes. 18098 feasible genes (genes that can be used in the analysis): - symbol: TM00000001 TM00000002 TM00000003 TM00000004 TM00000005 ... - 90 significant genes. GO graph (nodes with at least 0 genes): - a graph with directed edges - number of nodes = 1556 - number of edges = 1853 ------------------------- topGOdata object ------------------------- sessionInfo() R version 2.7.1 (2008-06-23) i686-pc-linux-gnu locale: LC_CTYPE=en_US.ISO-8859-15;LC_NUMERIC=C;LC_TIME=en_US.ISO-8859-15;LC_C OLLATE=en_US.ISO-8859-15;LC_MONETARY=C;LC_MESSAGES=en_US.ISO-8859-15;L C_PAPER=en_US.ISO-8859-15;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEA SUREMENT=en_US.ISO-8859-15;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] topGO_1.8.1 SparseM_0.78 GO.db_2.2.0 [4] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 [7] Biobase_2.0.1 graph_1.18.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 Hope that this helps, Adrian On Sun, Sep 14, 2008 at 8:02 AM, Heike Pospisil <pospisil at="" zbh.uni-hamburg.de=""> wrote: > Hi Adrian, > > thanks for your reply. > > I passed the annFUN.gene2GO and got no errors. allGo contains no NA and > no NULL. > go_list is a list of character vectors: > >> str(go_list2) > List of 9 > $ TM00000001: chr [1:2] "GO:0009058" "GO:0016757" > $ TM00000002: chr [1:38] "GO:0003700" "GO:0007275" "GO:0005634" "GO:0009414" > ... > $ TM00000003: chr [1:38] "GO:0003700" "GO:0007275" "GO:0045449" "GO:0005634" > ... > $ TM00000004: chr [1:5] "GO:0005634" "GO:0045449" "GO:0009943" "GO:0009947" > ... > $ TM00000005: chr [1:13] "GO:0016165" "GO:0040007" "GO:0006952" "GO:0009695" > ... > $ TM00000006: chr [1:38] "GO:0003700" "GO:0007275" "GO:0045449" "GO:0005634" > ... > $ TM00000007: chr [1:38] "GO:0003700" "GO:0007275" "GO:0045449" "GO:0005634" > ... > $ TM00000009: chr [1:42] "GO:0016301" "GO:0004672" "GO:0004674" "GO:0009733" > ... > $ TM00000010: chr [1:8] "GO:0009736" "GO:0005886" "GO:0004673" "GO:0009884" > ... > > And, here is my sessionInfo: > >> sessionInfo() > R version 2.7.2 (2008-08-25) > i486-pc-linux-gnu > > locale: > LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_ DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_D E.UTF-8;LC_NAME=de_DE.UTF-8;LC_ADDRESS=de_DE.UTF-8;LC_TELEPHONE=de_DE. UTF-8;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=de_DE.UTF-8 > > attached base packages: > [1] splines grid tcltk tools stats graphics grDevices > [8] utils datasets methods base > other attached packages: > [1] maizeprobe_2.2.0 matchprobes_1.12.1 maizecdf_2.2.0 [4] > GO_2.2.0 topGO_1.8.1 SparseM_0.78 [7] > biomaRt_1.14.1 RCurl_0.9-4 GOstats_2.6.0 [10] > Category_2.6.0 genefilter_1.20.0 survival_2.34-1 [13] > RBGL_1.16.0 annotate_1.18.0 xtable_1.5-3 [16] > GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.7-0 [19] DBI_0.2-4 > graph_1.18.1 qvalue_1.14.0 [22] maanova_1.10.0 > arrayQuality_1.18.0 RColorBrewer_1.0-2 [25] gridBase_0.4-3 > hexbin_1.14.0 colorspace_0.95 [28] convert_1.16.0 > marray_1.18.0 tkWidgets_1.18.0 [31] DynDoc_1.18.0 > widgetTools_1.16.0 statmod_1.3.6 [34] vsn_3.6.0 > lattice_0.17-14 affy_1.18.2 [37] preprocessCore_1.2.1 > affyio_1.8.1 Biobase_2.0.1 [40] limma_2.14.6 > rkward_0.4.9 > loaded via a namespace (and not attached): > [1] cluster_1.11.11 XML_1.96-0 > > Would be very glad if you have any idea, what went wrong. Thanks, > Heike > > > Adrian Alexa schrieb: >> >> Hi Heike, >> >> it seems that there is a problem with the go_list object. It should be >> a list of character vectors. However, it is hard to tell what is wrong >> with just the information you provided. Please also post the session >> info such that we know which version of the software are you using. >> >> The error is with the annFUN.gene2GO() function. if the go_list is >> correct, than the following line should pass without error: >> >> go2genes <- annFUN.gene2GO(whichOnto = "MF", gene2GO = go_list) >> >> If you get an error here, can you post the results of the following lines: >> >> allGO = unlist(go_list, use.names = FALSE) >> str(allGO) >> sumis.na(allGO)) >> sum(is.null(allGO)) >> >> >> Regards, >> Adrian >> >> >> >> >> >> >> On Fri, Sep 12, 2008 at 11:42 AM, Heike Pospisil >> <pospisil at="" zbh.uni-hamburg.de=""> wrote: >> >>> >>> Hello list, >>> >>> I am trying to use topGO for GO enrichment analysis. I have data from an >>> array which is still not supported by BioC (maize array). >>> >>> I have a mapping of genes to GO terms named go_list: >>> >>> $TM00000001 >>> [1] "GO:0009058" "GO:0016757" >>> >>> $TM00000002 >>> [1] "GO:0003700" "GO:0007275" "GO:0005634" "GO:0009414" "GO:0016563" >>> [6] "GO:0009737" "GO:0045449" "GO:0010072" "GO:0046982" "GO:0009651" >>> [11] "GO:0009733" "GO:0009723" "GO:0009734" "GO:0048527" "GO:0042803" >>> [16] "GO:0009867" "GO:0010150" "GO:0009825" "GO:0009908" "GO:0003713" >>> [21] "GO:0051607" "GO:0009790" "GO:0010014" "GO:0048467" "GO:0030528" >>> [26] "GO:0009741" "GO:0009735" "GO:0010089" "GO:0009834" "GO:0009901" >>> [31] "GO:0009611" "GO:0008361" "GO:0009416" "GO:0009620" "GO:0009744" >>> [36] "GO:0009753" "GO:0009751" "GO:0010199" >>> >>> Moreover, the geneList is the named factor that indicates which genes are >>> interested: >>> >>>> >>>> str(geneList) >>>> >>> >>> Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ... >>> - attr(*, "names")= chr [1:56321] "MZ00000001" "MZ00000002" "MZ00000003" >>> "MZ00000004" ... >>> >>> I have used annFUN.gene2GO as an annotation function: >>> >>> >>> GOdata<-new("topGOdata",ontology="MF",allGenes=geneList,annot=annF UN.gene2GO,gene2GO=go_list) >>> >>> Unfortunately, I got the following error message: >>> Building most specific GOs .....Error in order(allGO) : argument 1 is not >>> a >>> vector >>> >>> Does anybody have an idea what is wrong in my code? >>> >>> Thanks and best, >>> Heike >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> > >