What happens if you do annFUN.GO2genes(GO2genes = myGO2genes)? I don't think you need Entrez Gene IDs for topGO. What I don't understand is the weird mappings you are getting below. Best, Jim BTW, have you emailed Adrian Alexa directly? Not sure how closely he follows BioC help. Sebastien Gerega wrote: > Hi, > actually after attempting with what I thoguht were the correct > parameters I obtained the following error: > > Building most specific GOs .....Error in annotationFun(ontology, > .Object at allGenes, ...) : > unused argument(s) (GO2genes = list("162.m02116" = 2403, "162.m02150" = > 2403, "162.m02156" = c(1133, 2157, 9), "162.m02171" = 1199, "162.m02176" > = c(2157, 1133, 9), "162.m02195" = 9, "162.m02197" = c(1199, 2403), > "162.m02200" = c(1501, 1114, 3855, 1161, 1156, 3390, 1195), "162.m02222" > = c(208, 409, 1185), "162.m02236" = c(410, 8, 1217, 3569), "162.m02241" > = c(1133, 9, 2157), "162.m02255" = c(277, 1133), "162.m02262" = c(1561, > 2283), "162.m02279" = c(392, 1156), "162.m02281" = c(1301, 1143, 1302, > 1297), "162.m02286" = 2403, > > Perhaps this is to do with the annFUN.gene2GO function I used. I am not > sure how to alter the function (if necessary) for my gened IDs. Do the > gene IDs have to ben Entrez IDs or does that not matter? > thanks, > Sebastien > > James W. MacDonald wrote: >> Hi Sebasien, >> >> Sebastien Gerega wrote: >>> Hi, >>> I would like to identify overrepresented GO in my dataset using the >>> topGO package. >>> I am working with a C. neoformans oligo array and have the GO >>> annotation in a list with the following format: >>> >>> $`162.m02116` >>> [1] GO:0009536 >>> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 >>> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861 >>> >>> $`162.m02150` >>> [1] GO:0009536 >>> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 >>> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861 >>> >>> $`162.m02156` >>> [1] GO:0005554 GO:0008372 GO:0000004 >>> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 >>> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861 >>> >>> How do I go about creating the GOdata object? >>> >>> GOdata = new("topGOdata", >>> ontology = "MF", >>> allGenes = selectedList, >>> annot = annFUN.GO2genes, ## the new annotation function >>> GO2genes = myGO2genes) ## the GO to gene ID's dataset >>> >>> Specifically what do I use for the annotation function? It is unclear >>> to me how to write this aspect. >> >> The documentation is a bit unclear, but I believe you have things set >> up correctly. I assume you have done the rest of the analysis and had >> no errors? >> >> Best, >> >> Jim >> >> >>> Am I correct in understanding that I supply my list as the final >>> argument? >>> thanks, >>> Sebastien >>> >>> _______________________________________________ >>> 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 >> > -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

Hi Sebastien, I haven't been using topGO for a long time and I also depend on a custom annotation. I think I figured out how to do this, but there might be some mistake that I haven't recognized yet. I think that you are getting this error because the GO2genes is not present on your annotation function. My understanding is that the annotation function is supposed to give you a list where the names of the list are the GO categories and the components of the list are the gene identifiers. For instance, when I use my annotation function I get: > my.go.function("BP",names(geneList),list.annotation) $`GO:0000003` [1] "CK743206" "CK571803" "CO583848" "BQ108196" "CK591451" "CK591731" "CK592215" $`GO:0000022` [1] "CK594625" "CK571614" "CK571618" "CK571711" "CK571828" "BF024115" [7] "BF024122" "BF024255" "BF023849" "BF023957" "BF024087" "BE188450" [13] "CK572914" "CK591204" "CK592173" $`GO:0000045` [1] "CK572330" $`GO:0000077` [1] "CK591657" $`GO:0000079` [1] "BQ108504" The function that I use takes three arguments. The first one is the type of ontology (BP, MF or CC). The second one is a vector containing the identifiers of the genes that I am using. The third one is a list containing the three ontologies and within each ontology another list containing the genes and their GO numbers. For example: > head(names(geneList)) [1] "CK570393" "CK570476" "CK570477" "CK570482" "CK570483" "CK570484" > names(list.annotation) [1] "BP" "MF" "CC" > list.annotation$BP[1:3] $CK570482 [1] "GO:0008088" $CK570483 [1] "GO:0006412" "GO:0043039" $CK570484 [1] "GO:0016310" "GO:0006096" "GO:0001666" And the code for the function that I use is: my.go.function <- function(selected.ontology=c("BP","MF","CC"),the.genes,go.source) { if(class(go.source)!="list"&length(go.source)!=3) { stop("The go.source should be a list with the three GOs in it") } if(class(the.genes)!="character") { stop("The the.genes should be a vectors of gene names") } if(selected.ontology=="BP") { go.source <- go.source[[1]] } if(selected.ontology=="MF") { go.source <- go.source[[2]] } if(selected.ontology=="CC") { go.source <- go.source[[3]] } selected.genes <- unlist(sapply(the.genes,function(x){grep(x,names(go.source))})) genes.to.use <- go.source[selected.genes] genes.to.use.df <- as.data.frame(cbind(rep(names(genes.to.use),lapply(genes.to.use,length )),as.vector(unlist(genes.to.use)))) genes.to.use.df[,1] <- as.character(genes.to.use.df[,1]) genes.to.use.df[,2] <- as.factor(genes.to.use.df[,2]) return(split(genes.to.use.df[,1],genes.to.use.df[,2])) } I hope this helps. All the best, Artur Veloso On Thu, May 29, 2008 at 8:40 PM, Sebastien Gerega <seb@gerega.net> wrote: > Hi, > actually after attempting with what I thoguht were the correct parameters I > obtained the following error: > > Building most specific GOs .....Error in annotationFun(ontology, > .Object@allGenes, ...) : > unused argument(s) (GO2genes = list("162.m02116" = 2403, "162.m02150" = > 2403, "162.m02156" = c(1133, 2157, 9), "162.m02171" = 1199, "162.m02176" = > c(2157, 1133, 9), "162.m02195" = 9, "162.m02197" = c(1199, 2403), > "162.m02200" = c(1501, 1114, 3855, 1161, 1156, 3390, 1195), "162.m02222" = > c(208, 409, 1185), "162.m02236" = c(410, 8, 1217, 3569), "162.m02241" = > c(1133, 9, 2157), "162.m02255" = c(277, 1133), "162.m02262" = c(1561, 2283), > "162.m02279" = c(392, 1156), "162.m02281" = c(1301, 1143, 1302, 1297), > "162.m02286" = 2403, > > Perhaps this is to do with the annFUN.gene2GO function I used. I am not > sure how to alter the function (if necessary) for my gened IDs. Do the gene > IDs have to ben Entrez IDs or does that not matter? > thanks, > Sebastien > > > James W. MacDonald wrote: > >> Hi Sebasien, >> >> Sebastien Gerega wrote: >> >>> Hi, >>> I would like to identify overrepresented GO in my dataset using the topGO >>> package. >>> I am working with a C. neoformans oligo array and have the GO annotation >>> in a list with the following format: >>> >>> $`162.m02116` >>> [1] GO:0009536 >>> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 >>> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861 >>> >>> $`162.m02150` >>> [1] GO:0009536 >>> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 >>> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861 >>> >>> $`162.m02156` >>> [1] GO:0005554 GO:0008372 GO:0000004 >>> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 >>> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861 >>> >>> How do I go about creating the GOdata object? >>> >>> GOdata = new("topGOdata", >>> ontology = "MF", >>> allGenes = selectedList, >>> annot = annFUN.GO2genes, ## the new annotation function >>> GO2genes = myGO2genes) ## the GO to gene ID's dataset >>> >>> Specifically what do I use for the annotation function? It is unclear to >>> me how to write this aspect. >>> >> >> The documentation is a bit unclear, but I believe you have things set up >> correctly. I assume you have done the rest of the analysis and had no >> errors? >> >> Best, >> >> Jim >> >> >> Am I correct in understanding that I supply my list as the final >>> argument? >>> thanks, >>> Sebastien >>> >>> _______________________________________________ >>> 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 >>> >> >> > _______________________________________________ > 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]]