hello list: I am using the package "topGO" to analyse GO enrichment of gene sets: and I following the example of topGO 1.2.1package document ( http://www.bioconductor.org/packages/2.0/bioc/vignettes/topGO/inst/doc /topGO.pdf) as follow: ---------------------------------------------------------------------- ---------------------------------------------------------------------- ------------------------------------- library(topGO); library(ALL); data(ALL); BPterms <- ls(GOBPTerm); str(BPterms); affyLib <- paste(annotation(ALL), "db", sep = "."); library(package = affyLib, character.only = TRUE); library(genefilter); f1 <- pOverA(0.25, log2(100)); f2 <- function(x) (IQR(x) > 0.5); ff <- filterfun(f1, f2); eset <- ALL[genefilter(ALL, ff), ]; geneNames <- featureNames(eset); length(geneNames); myInterestedGenes <- sample(geneNames, 100); geneList <- factor(as.integer(geneNames %in% myInterestedGenes)); names(geneList) <- geneNames; str(geneList); GOdata <- new("topGOdata", ontology = "MF", allGenes = geneList, annot = annFUN.hgu, affyLib = affyLib); ---------------------------------------------------------------------- ---------------------------------------------------------------------- -------------------- but report that *Building most specific GOs .....Error in .local(.Object, ...) : object "annFUN.db" not found* if I change the annot = annFUN.db to the function annFUN.hgu, which report in the topGO, but the another error report : * Building most specific GOs .....Error in get(paste(affyLib, "GO2PROBE", sep = "")) : variable "hgu95av2.dbGO2PROBE" was not found *could someone told me why , thanks [[alternative HTML version deleted]]

Hello, there is probably some issue with incompatible package versions, since you seem to be using a very old version of topGO. Please always attach the output of sessionInfo() to your questions to this list. You should the install the newest version of R (R-2.7.2) and then update all used packages to the current version, see http://www.bioconductor.org/docs/install/ If the problem persists with the new versions, please get back to the list, but my guess is that your problem should be resolved after the installation. Regards, Joern goodgood wrote: > hello list: > I am using the package "topGO" to analyse GO enrichment of gene sets: > and I following the example of topGO 1.2.1package document ( > http://www.bioconductor.org/packages/2.0/bioc/vignettes/topGO/inst/d oc/topGO.pdf) > > > as follow: > -------------------------------------------------------------------- ---------------------------------------------------------------------- --------------------------------------- > library(topGO); > library(ALL); > data(ALL); > BPterms <- ls(GOBPTerm); > str(BPterms); > > affyLib <- paste(annotation(ALL), "db", sep = "."); > library(package = affyLib, character.only = TRUE); > > library(genefilter); > f1 <- pOverA(0.25, log2(100)); > > f2 <- function(x) (IQR(x) > 0.5); > ff <- filterfun(f1, f2); > eset <- ALL[genefilter(ALL, ff), ]; > > geneNames <- featureNames(eset); > length(geneNames); > > myInterestedGenes <- sample(geneNames, 100); > geneList <- factor(as.integer(geneNames %in% myInterestedGenes)); > names(geneList) <- geneNames; > str(geneList); > > GOdata <- new("topGOdata", ontology = "MF", allGenes = geneList, annot = > annFUN.hgu, affyLib = affyLib); > > -------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------- > but report that > > *Building most specific GOs .....Error in .local(.Object, ...) : object > "annFUN.db" not found* > > if I change the annot = annFUN.db to the function annFUN.hgu, which report > in the topGO, but the another error report : > * > Building most specific GOs .....Error in get(paste(affyLib, "GO2PROBE", sep > = "")) : > variable "hgu95av2.dbGO2PROBE" was not found > > *could someone told me why , > thanks > >