Hi All I am trying to build an annotation library for some in-house plant microarrays using AnnBuilder. I have a base file that consists of a column of probe names, and nearest matches to NCBI genes. I have installed entrex files, unigene files and go files locally to speed the process. I am trying to map the plant probes on the microarray to rice genes in UniGene. I run the following script: library("AnnBuilder") myBase<-("myFile") myDir<-tempdir() myBaseType="gb"; mySrcUrls<-c(EG="file:///home/rc69/R/AnnBuilder/gene/DATA", LL="file:///home/rc69/R/AnnBuilder/LocusLink/Archive/LL_tmpl.gz", UG ="file:///home/rc69/R/AnnBuilder/repository/UniGene/Homo_sapiens/Hs.da ta.gz", GO="file:///home/rc69/R/AnnBuilder/Go/Latest") date() if(.Platform$OS != "windows" && interactive()){ ABPkgBuilder(baseName=prgBase, srcUrls=mySrcUrls, baseMapType=myBaseType, pkgName="myPRG_Pkg", pkgPath=myDir, organism="Oryza sativa", version="1.1.0", author=list(author="Ross", maintainer="Ross"), fromWeb=FALSE)} The code runs well for about 7 minutes, then fails and returns the following error: Error in allis.na(annotation[, "GO"])) : subscript out of bounds. I am using the latest version of the GO files: go_200603-termdb.rdf-xml.gz Does anyone have any suggestions of the nature of the problem and how I might fix it. Many thanks for your help Ross Dr Ross Chapman Bioinformatician Senior Research Scientist Computational Biology and Discovery Technologies Plant Genetics and Genomics Research Platform Department of Primary Industries Victorian Agribiosciences Centre 1 Park Drive, Bundoora, Victoria, 3083 Australia

Hi Ross, ABPkgBuilder depends on the GO annotation data package. If you want to use the latest data from the GO website, I would try first creating your own updated GO package (uses a different part of AnnBuilder). I'm not certain, but that is my first guess at what is going wrong. + seth

Hi Ross, I believe that this bug had been fixed in the developmental version. Please upgrade your AnnBuilder to the developmental version and you won't see this error any more. HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Fri, 17 Mar 2006 ross.chapman at dpi.vic.gov.au wrote: > Hi All > > I am trying to build an annotation library for some in-house plant > microarrays using AnnBuilder. > > I have a base file that consists of a column of probe names, and nearest > matches to NCBI genes. > > I have installed entrex files, unigene files and go files locally to speed > the process. > > I am trying to map the plant probes on the microarray to rice genes in > UniGene. > > I run the following script: > > library("AnnBuilder") > myBase<-("myFile") > myDir<-tempdir() > myBaseType="gb"; > mySrcUrls<-c(EG="file:///home/rc69/R/AnnBuilder/gene/DATA", > LL="file:///home/rc69/R/AnnBuilder/LocusLink/Archive/LL_tmpl.gz", > UG > ="file:///home/rc69/R/AnnBuilder/repository/UniGene/Homo_sapiens/Hs. data.gz", > GO="file:///home/rc69/R/AnnBuilder/Go/Latest") > date() > if(.Platform$OS != "windows" && interactive()){ > ABPkgBuilder(baseName=prgBase, srcUrls=mySrcUrls, baseMapType=myBaseType, > pkgName="myPRG_Pkg", pkgPath=myDir, > organism="Oryza sativa", version="1.1.0", author=list(author="Ross", > maintainer="Ross"), fromWeb=FALSE)} > > The code runs well for about 7 minutes, then fails and returns the > following error: > > Error in allis.na(annotation[, "GO"])) : subscript out of bounds. > > I am using the latest version of the GO files: > > go_200603-termdb.rdf-xml.gz > > Does anyone have any suggestions of the nature of the problem and how I > might fix it. > > Many thanks for your help > > Ross > > > Dr Ross Chapman > Bioinformatician > Senior Research Scientist > Computational Biology and Discovery Technologies > Plant Genetics and Genomics Research Platform > Department of Primary Industries > Victorian Agribiosciences Centre > 1 Park Drive, Bundoora, Victoria, 3083 > Australia > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >