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&maps cale=&show_description=show http://www.kegg.jp/kegg-bin/show_pathway?org_name=aag&mapno=00020&maps cale=&show_description=show Then I ran this command: makeSPIAdata(kgml.path="C:\\Users\\David\\Desktop\\aag_kegg\\",organis m="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\\D avid\\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 [[alternative HTML version deleted]]

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.007 9217 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&maps cale=&show_description=show http://www.kegg.jp/kegg-bin/show_pathway?org_name=aag&mapno=00020&maps cale=&show_description=show Then I ran this command: makeSPIAdata(kgml.path="C:\\Users\\David\\Desktop\\aag_kegg\\",organis m="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\\D avid\\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 [[alternative HTML version deleted]]