[BioC] adding KEGG annotations with ABPkBuilder from E.coli

Marc Carlson mcarlson at fhcrc.org
Sat Nov 8 02:35:03 CET 2008

Hi Robert,

I have just merged a patch into place for this.  You should be able to
get a new version of both the annotate and Category packages soon which
should resolve this.  Please let me know if there are any other issues.


Robert Castelo wrote:
> hi all,
> i'm trying to build an annotation package for the Ecoli_ASv2 affy chip
> and one of the things that i have not succeed to obtain is to
> incorporate the available pathway annotations from KEGG.
> the problem seems to be within the function ABPkBuilder (from the
> AnnBuilder package), when it calls 'getAnnData' and this functions does
> the following line of code:
>         pathNEnzyme <- try(mapLL2ECNPName(srcObjs[["kegg"]]))
> which runs smoothly without any problem but the resulting object called
> pathNEnzyme is not using EntrezGeneIDs but the so-called Blattner IDs,
> which are commonly used to refer to E.coli genes, and this must arise
> from how KEGG stores pathway information for E.coli.
> I guess this is what afterwards bans the process of succeeding because
> it tries to join these Blattner IDs (using the R function merge) with
> the rest of the annotations based on EntrezGeneIDs.
> I can easily map Blattner IDs with EntrezGeneIDs but I don't know how to
> tell ABPkBuilder to use these two sources of IDs to build the annotation
> package, any idea?
> thanks!!
> robert.
> ps: here goes my sessionInfo():
> R version 2.6.0 (2007-10-03) 
> x86_64-unknown-linux-gnu 
> locale:
> C
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets
> methods  
> [8] base     
> other attached packages:
> [1] GO_2.0.1            AnnBuilder_1.16.0   annotate_1.16.1    
> [4] xtable_1.5-2        AnnotationDbi_1.0.6 RSQLite_0.6-4      
> [7] DBI_0.2-4           XML_1.93-2          Biobase_1.16.1     
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-15

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