[BioC] Pathway Analyis for C-difficile microarrays

[Claus Mayer]

Hello!

I am working on a data set using C-difficile two-color microarrays and would
like to do some pathway analysis. KEGG has quite a number of pathways for
this organism (see
http://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=cdf),
but when I tried to access them with KEGG.db (version 2.4.5, R 2.12.0) I had
no success, e.g. if I type "KEGGPATHID2EXTID$hsa00010" I do get a list of
genes present in the human Glycolysis / Gluconeogenesis pathway but typing
"KEGGPATHID2EXTID$cdf00010" doesn't produce any output for the corresponding
C-difficile pathway (though both of them are present in KEGG).

For a single small pathway I could of course create a list with gene ids per
hand by copying the gene list from KEGG, but of course it would be more
convenient if I could do this automatically with Bioconductor.

Has any of you clever people worked with C-difficile arrays and performed
pathway analysis on them? And if so, how did you do it? 

Thanks

Claus