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

[Robert Castelo]

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

-- 
Robert Castelo, PhD
RyC Fellow Researcher
Dept. Experimental and Health Sciences
Pompeu Fabra University
Barcelona Biomedical Research Park
Dr. Aiguader 88
E-08025 Barcelona, Spain
tel +34 933 160 514
fax +34 933 160 550
robert.castelo at upf.edu