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The sample-by-location interaction term was tested for significance.
The contribution of each explanatory term was tested sequentially, with non-significant terms removed from the model to produce the minimal model following standard stepwise deletion [43].
This was done using a conditional hypergeometric test; conditioning means that each term was tested for statistical overrepresentation after removing genes that overlapped a significant child term.
Over-representation of each term was tested using the binomial distribution (an efficiently computable and close approximation to the hypergeometric distribution when the number of items to choose among is large [20]).
No interaction term was tested.
The enriched GO term was tested by using the hypergeometric distribution.
Similar(42)
Each of the three interaction terms was tested in turn with a single joint test.
A broad list of search terms was tested to identify terms that produced relevant articles and minimized redundancy.
The difference in the frequency of pathway annotation terms was tested by Fisher's exact probability test (P < 0.05).
The difference in the frequency of GO terms was tested by Fisher's exact probability test (P < 0.01).
Enrichment of GO terms was tested with Fisher's exact test, using the Bioconductor package topGO version 0.9.7 [ 58, 59].
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CEO of Professional Science Editing for Scientists @ prosciediting.com