[BioC] GO and Annotation

Mayte Suarez-Farinas mayte at babel.rockefeller.edu
Mon May 3 21:26:52 CEST 2004

Dear Collegues:

I built an annotation package (using AnnBuilder) to work with mu11KsubA 
and B Chips. See below the  script:

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 at 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.

Error in get(x, envir, mode, inherits) : variable "GO:0050983" was not 
> 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??

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