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Why should I use a background set in evaluating enrichments?

Statistical enrichments are always relative to some background set. If you do not provide a background set, then GREAT uses a whole genome background. Such a background is not always appropriate. You should provide a background set to account for any inherent biases in sampling1 .

References

Footnotes
Ref Notes
1 Rhee S. Y. et al. Use and misuse of the gene ontology annotations, Nat Rev Genet. 9:509-515 (2008).
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