Matrix for a Fisher's exact test
I want to make Fisher's exact test. I've got the number of active genes in a sample involved in EMT pathway, non-active genes, number of all the genes in a pathway and number of all the genes in a sample. Can please someone explain to me how should I place these numbers in a matrix to make Fisher's exact test?
It is 118 active, 23 non-active, 13015 in a sample and 185 in a pathway
2 answers
The typical test for this is a hypergeometric test, not Fisher or Chi Square. See here a response from the author of clusterProfiler on exactly what you're asking: Issues with enricher() function from clusterProfiler
This site is quite easy to use to calculate it: https://www.langsrud.com/fisher.htm
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