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","UniGe ne.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@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??

> >anntable<-aafTableAnn(probesids,chip=AnnPkg,aaf.handler()) >Error in get(x, envir, mode, inherits) : variable "GO:0050983" was not >found For any platfoem specific data packages built using ABPkgBuilder, the above may occur due to two reasons: 1. The data sources used to build the platform specific package (e. g. mu11KsubA in this case) and the GO package are off sync (e. g. built at different times) so that GO ids that are found in one package may not exist in the other. 2. Alias GO ids (GO ids that become alias of primary GO ids due to merges) are used by the source data used to build the platform specific data package. We are in the process of improving the GO package so that alias GO ids can be better handled. >> 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?? > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

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@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","UniGe ne.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@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?? _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor