[BioC] GOstats error messages

[Ting-Yuan Liu (FHCRC)]

Hi Mark,

This problem is due to a bug in AnnBuilder.  Simply speaking, AnnBuilder 
can not handle probeset ids with "#".  This bug is fixed.  The annotation 
packages in the coming release will not cause this kind of problem.  

Thanks for reporting this bug.  

Ting-Yuan

On Tue, 20 Sep 2005, Kimpel, Mark William wrote:

> 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")
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> -- 
> 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
> 
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