Hi
I am trying to run a GO enrichment test on genes identified in experiments on an 
affymetrix hgu133plus2 chip. I get zero annotations, even though within hgu133plus2.db 
I can find annotations for the genes of interest. I've spent a while trying to get it to
work but with no success. What (no doubt very basic thing) am I doing wrong?

Best
Will

library_calls <- function() {
    library('hgu133plus2.db')
    library('topGO')
}

get_gene_universe <- function(affy_library) {

    # get all entrez ids associated with this chip
    gene_universe     = as.integer(keys(eval(parse(text = affy_library)), keytype='ENTREZID'))

    return(gene_universe)
}

probesets_to_entrez <- function(probeset_keys, affy_library) {

    # get entrez ids for each of these 
    entrez_ids_df     = select(eval(parse(text = affy_library)), probeset_keys, 'ENTREZID', 'PROBEID')

    # return unique
    entrez_ids         = unique(entrez_ids_df$ENTREZID)

    # remove any NAs
    entrez_ids         = as.integer(entrez_ids[!is.na(entrez_ids)])

    return(entrez_ids)
}

find_GO_terms_for_probesets <- function(probeset_keys, affy_library) {
    # get GO ids for each of these 
    GO_ids_df         = select(eval(parse(text = affy_library)), probeset_keys, 'GO','PROBEID')

    # restrict to BP
    GO_ids             = unique(GO_ids_df[GO_ids_df$ONTOLOGY == 'BP', 'GO'])

    # check for annotations
    select(GO.db, keys = GO_ids, columns = 'DEFINITION', keytype = 'GOID')
}

# admin
library_calls()

# define library
affy_library     = 'hgu133plus2.db'
# define test keys
probeset_keys = c('201060_x_at', '213558_at', '223294_at', '201061_s_at', '202976_s_at', '224177_s_at')

# get gene universe in entrez ids
gene_universe     = get_gene_universe(affy_library)

# get genes of interest in entrez ids
gene_list         = probesets_to_entrez(probeset_keys, affy_library)

# define inputs to topGOdata creator
gene_vector         = factor(as.integer(gene_universe %in% gene_list))
names(gene_vector)     = gene_universe

# check that GO terms exist
find_GO_terms_for_probesets(probeset_keys, affy_library)
#         GOID
# 1  GO:0051260  The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
# 2  GO:1901585                                                                                                                                                                              Any process that modulates the frequency, rate or extent of acid-sensing ion channel activity.
# 3  GO:0007010                                                                                                             A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
# ...

# create new topGOdata object
GOdata_BP = new("topGOdata", 
    ontology         = 'BP', 
    allGenes         = gene_vector, 
    annotationFun     = annFUN.db, 
    affyLib         = affy_library
    )

# Fails:
# Building most specific GOs .....    ( 0 GO terms found. )

# Build GO DAG topology ..........    ( 0 GO terms and 0 relations. )
# Error in if (is.na(index) || index < 0 || index > length(nd)) stop("vertex is not in graph: ",  : 
#   missing value where TRUE/FALSE needed

sessionInfo()
# R version 3.1.2 (2014-10-31)
# Platform: x86_64-w64-mingw32/x64 (64-bit)

# locale:
# [1] LC_COLLATE=German_Switzerland.1252  LC_CTYPE=German_Switzerland.1252    LC_MONETARY=German_Switzerland.1252
# [4] LC_NUMERIC=C                        LC_TIME=German_Switzerland.1252    

# attached base packages:
# [1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

# other attached packages:
#  [1] topGO_2.18.0         SparseM_1.05         GO.db_3.0.0          graph_1.44.0         hgu133plus2.db_3.0.0
#  [6] org.Hs.eg.db_3.0.0   RSQLite_1.0.0        DBI_0.3.1            AnnotationDbi_1.28.1 GenomeInfoDb_1.2.2  
# [11] IRanges_2.0.0        S4Vectors_0.4.0      Biobase_2.26.0       BiocGenerics_0.12.0 

# loaded via a namespace (and not attached):
# [1] grid_3.1.2      lattice_0.20-29 tools_3.1.2   

I believe you are missing the genSel argument when you are creating your topGO object (which IIRC should be your gene_vector, and allGenes should be your gene_universe).

OK, thanks for trying to help! I think what you've now suggested was what I was originally doing in the example I posted - I'd previously had success using gene_vector as a boolean vector, converted to a factor, but with a different chip.

Thanks for the suggestion of GOstats. I'll try anything which seems likely to work...