Hi All I have constructed an annotation library for a custom cDNA microarray using AnnBuilder. I went to analyse results from experiments using these microarrays using GOHyperG in GOstats but got an error stating that there was no GO2ALLPROBES object. The objects that have been created by my AnnBuilder excerise are: ls("package:PRGproteinpkg") [1] "PRGproteinpkg" "PRGproteinpkgACCNUM" "PRGproteinpkgLOCUSID" [4] "PRGproteinpkgMAPCOUNTS" "PRGproteinpkgORGANISM" "PRGproteinpkgQC" [7] "PRGproteinpkgQCDATA" The code I used for creating the annotation library using AnnBuilder is as follows: library("AnnBuilder") myBase<-file.path("PRG_NCBI_mappings.txt") myBaseType="gb"; myDir<-tempdir() 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/Oryza_sativa/Os.da ta.gz", GO="file:///home/rc69/R/AnnBuilder/Go/Latest") date() if(.Platform$OS.type != "windows" && interactive()){ ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls, baseMapType=myBaseType, pkgName="PRG_protein_pkg", pkgPath=myDir, organism="Oryza sativa", version="1.1.0", author=list(author="Ross", maintainer="ross.chapman at xxxxxxxx"), fromWeb=FALSE)} date() Can anyone advise me how I might create the necessary GO2ALLPROBES annotation. I have searched the AnnBuilder and GOstats vignettes but have not been able to find a solution. Many thanks in advance 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, Try myBaseType="gbNRef" 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, 24 Mar 2006 ross.chapman at dpi.vic.gov.au wrote: > Hi All > > I have constructed an annotation library for a custom cDNA microarray using > AnnBuilder. > > I went to analyse results from experiments using these microarrays using > GOHyperG in GOstats but got an error stating that there was no GO2ALLPROBES > object. > > The objects that have been created by my AnnBuilder excerise are: > > ls("package:PRGproteinpkg") > [1] "PRGproteinpkg" "PRGproteinpkgACCNUM" > "PRGproteinpkgLOCUSID" > [4] "PRGproteinpkgMAPCOUNTS" "PRGproteinpkgORGANISM" "PRGproteinpkgQC" > [7] "PRGproteinpkgQCDATA" > > The code I used for creating the annotation library using AnnBuilder is as > follows: > > library("AnnBuilder") > myBase<-file.path("PRG_NCBI_mappings.txt") > myBaseType="gb"; > myDir<-tempdir() > 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/Oryza_sativa/Os. data.gz", > GO="file:///home/rc69/R/AnnBuilder/Go/Latest") > date() > if(.Platform$OS.type != "windows" && interactive()){ > ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls, baseMapType=myBaseType, > pkgName="PRG_protein_pkg", pkgPath=myDir, > organism="Oryza sativa", version="1.1.0", > author=list(author="Ross", maintainer="ross.chapman at xxxxxxxx"), > fromWeb=FALSE)} > date() > > Can anyone advise me how I might create the necessary GO2ALLPROBES > annotation. I have searched the AnnBuilder and GOstats vignettes but have > not been able to find a solution. > > Many thanks in advance > > 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 > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >