I want to know how affy probesets map to kegg pathways in drosophila2
However I realized that no such mappings are included in drosophila2
Is there a reason for this? Where can I find that information?
The short answer is: this is a bug/missing feature.
The package drosophila2 was built by using ABPkgBuilder, which is
human, mouse and rat, not for fly. To get probe to KEGG mapping, the
first gets probe to Entrez Gene mapping, and then use
to get KEGG pathway IDs. dem_gene_map.tab contains two columns: KEGG
and KEGG pathway IDs. KEGG has similar files for each organism. For
mouse and rat, KEGG Gene IDs happen to be the same as Entrez Gene ID.
function ABPkgBuilder can use this file to get probe to KEGG pathway
right away. But for other organisms KEGG gene IDs are in a different
Therefore ABPkgBuilder will fail to get KEGG pathway IDs.
One solution is to modify ABPkgBuilder to get Entrez Gene to KEGG gene
The other solution is to write specific builder functions for fly,
what happened to Arabidopsis and yeast. It is because ABPkgBuilder
Gene ID as the base identifier for gene. But most people may perfer
(rather than Entrez Gene). Therefore, it is more appealling to write a
specific builder function. But this is also time consuming...
sorry there is no direct answer, but hope it provides some background