[Bioc-devel] How to replace KEGG.db

[Claudio Lottaz]

Hi all,

In my package adSplit, I use microarray annotation packages like hgu95av2.db to find probes for pathways (in hgu95av2PATH2PROBE). In order to find names out of these KEGG identifiers, I use KEGG.db. However, KEGG.db is deprecated starting bioconductor 3.13 and bioconductor officials suggest to use KEGGREST instead. Unfortunatly, KEGGREST seems not to find information from these microarray annotation package IDs. E.g.:

library(hgu95av2.db)
library(KEGG.db)
library(KEGGREST)

path.id <- ls(hgu95av2PATH2PROBE)[1]
kegg.name <- KEGGPATHID2NAME[[path.id]]
print(kegg.name)

keggrest.info <- keggGet(path.id)
print(keggrest.info)

Does anybody have an idea, how to solve this?

Cheers and thanks,
Claudio