[BioC] GO and Annotation

[John Zhang]

>
>anntable<-aafTableAnn(probesids,chip=AnnPkg,aaf.handler())
>Error in get(x, envir, mode, inherits) : variable "GO:0050983" was not 
>found

For any platfoem specific data packages built using ABPkgBuilder, the above may 
occur due to two reasons:

1. The data sources used to build the platform specific package (e. g. mu11KsubA 
in this case) and the GO package are off sync (e. g. built at different times) 
so that GO ids that are found in one package may not exist in the other.

2. Alias GO ids (GO ids that become alias of primary GO ids due to merges) are 
used by the source data used to build the platform specific data package. We are 
in the process of improving the GO package so that alias GO ids can be better 
handled.




>> 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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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084