[BioC] Overrepresentation pathway with KEGGPROFILE and SPIA

[slzhao]

Hi Greg Montréal,

I am the author of KEGGprofile package. Thanks for using my package. I
think defining the reference genes based on your own experiments is
the most reasonable method for finding overrepresentation pathways.
For example, the high abundance proteins were easier to be identified
in a proteomics experiment because of the limitation of current
analysis method. If all of the proteins for the species were used as
reference to find the overrepresented pathways for significant changed
proteins, the pathways with high abundance proteins would be found. So
I think the proteins identified in this experiment is better reference
than all of the proteins for the species.
For the find_enriched_pathway function, we used genes but not chip ids
as input. So the function didn't know which chip was used in this
experiment. I think a parameter that was used to define reference
genes could be added in next version of this package.


-- 
              Shilin Zhao
Key Laboratory of Systems Biology
Shanghai Institute for Biological Sciences
Chinese Academy of Sciences
320 Yue-Yang Road
Shanghai,China,200031