Hi Dave,
SPIA (Signaling Pathway Impact Analysis) is for the analysis of signaling pathways. The ones you tried are metabolic (usually KEGG IDs for metabolic pathways look like 00***).
You can use other general gene set enrichment methods that do not use pathway topology information but can be applied to both signaling and metabolic pathways. See this paper
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0079217 that may help you choose another method among the ones available in Bioconductor.

Regards,
Adi

From: David Price [mailto:dave.p.price@gmail.com]
Sent: Friday, January 03, 2014 12:58 PM
To: Bioconductor@r-project.org; Tarca, Adi
Subject: makeSPIAdata

Hello,
I'm using SPIA version 2.14.0 and having a problem creating a SPIA RData file.
I've downloaded a series of kgml files for aedes aegypti using the Download KGML link on pathway pages, examples:
http://www.kegg.jp/kegg-bin/show_pathway?org_name=aag&mapno=00010&mapscale=&show_description=show
http://www.kegg.jp/kegg-bin/show_pathway?org_name=aag&mapno=00020&mapscale=&show_description=show
Then I ran this command:
makeSPIAdata(kgml.path="C:\\Users\\David\\Desktop\\aag_kegg\\",organism="aag",out.path="C:\\Users\\David\\Documents\\R\\win-library\\3.0\\SPIA\\extdata\\")
and got [1] FALSE as the result, and no aagSPIA.RData file was generated.

Then I tried this command on the example kgml files that downloaded with SPIA:
makeSPIAdata(kgml.path="C:\\Users\\David\\Documents\\R\\win-library\\3.0\\SPIA\\extdata\\keggxml\\hsa",organism="aag",out.path="C:\\Users\\David\\Documents\\R\\win-library\\SPIA\\extdata\\")
This resulted in [1] TRUE and an aagSPIA.RData file being generated.
The aag kgml files I downloaded seem to be intact and complete.  They are about 2 years newer than the example hsa files and it is possible something changed in the xml was a thought I had.
Any advice would be greatly appreciated.

Thanks,
Dave


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