
Dear All:


I have a question about the bioconductor goseq (http://www.bioconductor.org/packages/release/bioc/html/goseq.html) package for GO enrichment analysis (taking length bias into consideration). Those top-ranked categories are obtained based on the ranking of "over_represented_pvalues" from the goseq object. The goseq also includes "under_represented_pvalues" from the same output. Can I know how the "over/under-representations" are determined? Why don't we consider "under-representation"?


I am not sure if I can think of a category being "enriched" this way: if there are more DE genes for a particular category, then this category is "enriched" and the associated p-value is called "over-represented", while if there are fewer DE genes for a particular category, then this category is called "depleted" and "under-represented"? Can this be reflected in the sign (+/-) of certain quantities?


I am new to this area, so thank you very much for your help! The vignette of the goseq package can be found here (http://www.bioconductor.org/packages/2.8/bioc/vignettes/goseq/inst/doc/goseq.pdf).

Thanks!

Best,
-- 
Gu Mi
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