[BioC] GO and Annotation

[James MacDonald]

This just means that the particular GO term is not found in the current
GO package you have installed. You might try updating your GO package if
yours is more than a couple of months old (using update.packages2() in
reposTools).

HTH,

Jim



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

>>> Mayte Suarez-Farinas <mayte at babel.rockefeller.edu> 05/03/04 03:26PM
>>>

Dear Collegues:

I built an annotation package (using AnnBuilder) to work with mu11KsubA

and B Chips. See below the  script:

------------------------------------------------------------------------
library(AnnBuilder)
myDir<-tempdir()
Ann1<-read.table(file='/home/MyAnn/affy_Mu11KA',skip=1,header=TRUE,as.is=TRUE,sep='\t',quote='',comment.char="")
Ann2<-read.table(file='/home/MyAnn/affy_Mu11KB',skip=1,header=TRUE,as.is=TRUE,sep='\t',quote='',comment.char="")
Ann<-rbind(Ann1[,c("Probe.ID","UniGene.ID")],Ann2[,c("Probe.ID","UniGene.ID")])
write.table(as.matrix(Ann), file = file.path(myDir, "AnnDan"),sep =
"\t", row.names = FALSE, col.names = FALSE, quote=FALSE)
ABPkgBuilder(baseName=file.path(myDir, "AnnDan"),
srcUrls=getSrcUrl("ALL",organism='mouse'), baseMapType = 'ug',otherSrc =

NULL, pkgName="mu11KABannot", pkgPath=myDir, organism = "mouse",version
= "1.3.0", makeXML = TRUE, 
author = list(author = "MSF",maintainer =
"mayte at babel.rockefeller.edu"), fromWeb = TRUE)
------------------------------------------------
                                                                       
        

Then I install the package (using R CMD INSTAll.... ) and It was Ok.
But with some list of genes it fails. See example below using all the 
genes in Chips A B.

anntable<-aafTableAnn(probesids,chip=AnnPkg,aaf.handler())
Error in get(x, envir, mode, inherits) : variable "GO:0050983" was not

found
> aaf.handler()
 [1] "Probe"               "Symbol"              "Description"
 [4] "Function"            "Chromosome"          "Chromosome Location"
 [7] "GenBank"             "LocusLink"           "Cytoband"
[10] "UniGene"             "PubMed"              "Gene Ontology"
[13] "Pathway"

It works OK when you eliminate the GO column:

> anntable<-aafTableAnn(probesids,chip=AnnPkg,aaf.handler()[-12])

Did I make a mistake in the building procedure or it is something 
related with the internal extructure of GO package??

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