[BioC] object "annFUN.db" not found in topGO

[Joern Toedling]

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/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
>
>