makeSPIAdata
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David Price ▴ 10
@david-price-6308
Last seen 9.6 years ago
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]]
SPIA SPIA • 1.4k views
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Tarca, Adi ▴ 570
@tarca-adi-1500
Last seen 4 months ago
United States
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]]
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