[BioC] GOstats error messages

[James W. MacDonald]

Kimpel, Mark William wrote:
> 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.

I believe this problem is due to the rgu34a 1.8.4 package, in particular 
the rgu34aGO2ALLPROBES environment:

 > as.list(rgu34aGO2ALLPROBES)[[1]][1:10]
               <NA>                IDA                IEA 
  IEA               <NA>
   "rc_AA924909_at"      "S55427_s_at"      "S55427_s_at" 
"AJ001320_at" "AJ011656cds_s_at"
                IDA                IEA               <NA> 
  IEA                IEA
        "M74067_at"        "M74067_at"      "AJ011811_at" 
"AJ011811_g_at"      "AB005549_at"


None of these values is an Affymetrix ID - instead they appear to be a 
combination of a GenBank/RefSeq accession number and an Affy ID.

Best,

Jim



> 
> 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")
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623