[BioC] GOstats error messages

[Kimpel, Mark William]

I am still getting an Error Message when I use GOHyperG. The message
reads, "Error: value for 'L00981mRNA#2_at' not found". As you can see
from my script below, which replicates this error, that this Affy ID is
not on my original list. Please see my script below the sessionInfo to
replicate the error. Note that in my original post I mistakenly said
that I am using rat2302; I am actually using rgu34a.

Thanks,

Mark
########################################################################
####
My session info is:


R version 2.2.0, 2005-08-29, i386-pc-mingw32 

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"
"grDevices" "utils"     "datasets"  "base"     

other attached packages:
  hgu95av2    GOstats genefilter     xtable       RBGL   annotate
GO      graph      Ruuid    cluster     rgu34a      limma  rgu34acdf
multtest 
   "1.6.5"    "1.2.0"    "1.7.7"    "1.2-5"    "1.4.0"    "1.6.3"
"1.6.5"    "1.6.5"    "1.6.2"   "1.10.1"    "1.8.5"    "2.0.7"
"1.4.3"    "1.7.3" 
  survival       affy reposTools    Biobase 
    "2.18"    "1.7.2"    "1.6.2"    "1.7.0"
########################################################################
####

require(GOstats)

affyIDVec<- c("AB000362_at", "AB000517_s_at", "AB001453_at",
"AB001576_s_at", "AB002086_at")

annot.pckg<-"rgu34a"

LocusLinkVec<-c(rep(NA,length(affyIDVec)))

#map Affy IDs to Locus Link IDs

for (i in 1:length(affyIDVec))

    {
        LocusLinkVec[i]<-if(!is.na(unlist(mget(x=affyIDVec[i],
envir=get(paste(annot.pckg, "LOCUSID", sep = "")), mode = "any",
          ifnotfound = NA, inherits =
FALSE)))){unlist(mget(x=affyIDVec[i], envir=get(paste(annot.pckg,
"LOCUSID", sep = "")), mode = "any",
          ifnotfound = list(function(x) stop(paste("value for '",
         x, "' not found", sep = ""), call. = FALSE)), inherits =
FALSE))} else {"-"}
         
    }
    
#make LL vector unique and remove NA values

x<-LocusLinkVec

x<-as.numeric(unique(x))

o<-order(x)

x<-x[o]

if(is.na(x[length(x)])) {x<-x[1:(length(x) - 1)]}

#Perform GoHyperG

BP.hyperG<-GOHyperG(x, lib=annot.pckg, what="BP")