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Question: understanding topGO enrichment
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gravatar for michael.steffen
9 weeks ago by
michael.steffen0 wrote:

I am trying to understand how topGO decides a GO term is enriched. Specifically, I am trying to understand how terms not in my list (universal or my genes of interested with annotated GO terms) can be considered significant. 

Like the example below. That GO ID is not in any of my lists, so how is it significant? 

GO.ID Term Annotated Significant Expected classicFisher 
GO:0009235 cobalamin metabolic process 1 1 0.03 0.02536 

Thanks, Mike

ADD COMMENTlink written 9 weeks ago by michael.steffen0

If you want help, and in particular if you are implying that there is a bug (which is what you are doing), it's incumbent upon you to provide a small, self contained example that other people can run to show what you are seeing. In addition, you need to show the results of running sessionInfo().

ADD REPLYlink written 9 weeks ago by James W. MacDonald43k
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