[BioC] GOstats error messages

[Kimpel, Mark William]

Thanks Jim. The problem probably exists in the soon to be released
rgu34a 1.8.5 as well, as is tried both 1.8.4 and 1.8.5 with the same
results.

Mark

Mark W. Kimpel MD

 

 

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Tuesday, September 20, 2005 8:12 AM
To: Kimpel, Mark William
Cc: Bioconductor Newsgroup
Subject: Re: [BioC] GOstats error messages

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