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