[BioC] Build an Annotation with GO2ALLPROBES

[Ting-Yuan Liu]

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
>