[BioC] Build an Annotation with GO2ALLPROBES

[ross.chapman at dpi.vic.gov.au]

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