[BioC] GOstats error messages

[Kimpel, Mark William]

The fix to rgu34a to make it compatible with GOstats resulted in no
error messages this time around. Thanks so much for your very prompt
attention and excellent help.

Mark 

Mark W. Kimpel MD

 

 

-----Original Message-----
From: Ting-Yuan Liu (FHCRC) [mailto:tliu at fhcrc.org] 
Sent: Wednesday, September 21, 2005 2:01 AM
To: Kimpel, Mark William
Cc: James W. MacDonald; Bioconductor Newsgroup
Subject: Re: [BioC] GOstats error messages


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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