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Question: Gostats Hypergeometric tests for non model organisms Kegg pathway
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gravatar for Luo Weijun
3.2 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
Claire, You can try GAGE/Pathview for non-model organisms. They support ~3000 KEGG species. However, you need to have the full dataset instead of a pre-selected list of differentially expressed genes. Details at: http://www.bioconductor.org/packages/release/bioc/html/gage.html http://www.bioconductor.org/packages/release/bioc/html/pathview.html -------------------------------------------- Claire [guest] wrote: Hello I would like to run an hypergeometric testing on KEGG terms for non- model organism. When it comes to Goterm I always use Gostats where I can enter my "universe" list and then my "target" genes and it works really well. However, when it comes to Kegg pathways, I tried to use go stats again but it's based on the kegg.db which is outdated and as a result I get the following error: "Loading required package: KEGG.db Failed with error: ???package ???AnnotationDbi??? 1.24.0 is loaded, but >= 1.25.15 is required by ???KEGG.db?????? In addition: Warning message: package ???KEGG.db??? was built under R version 3.1.0 Error in .testKEGGFrame(x, organism) : None of elements in the 1st column of your data.frame object are legitimate KEGG IDs." Does anyone have any recommendations for Kegg enrichment analysis for non-model organism and /or how to do an hypergeometric test with R directly? Thanks a lot for your help CLaire
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