[R] Hypergeometric Relationship to Fisher's exact test

通常用來做Enrichment analysis的方法不外乎是
(1) Binomial distribution probability

(2) Hypergeometric probability  P[X ≥ x] 的機率

ex. We have total 38574 probes, significance have 14558, then we take 53 probes and get 33 probes significance

[R code ]:   
P[X ≥ 33] = P[X = 33]+P[X > 33] = 1-P[X ≤ 32]
dhyper(33, 14558, (38574-14558), 53 ) +
phyper(33, 14558, (38574-14558), 53, lower.tail = FALSE)
= 1 - phyper(32, 14558, (38574-14558), 53)

而此Hypergeometric 機率又與Fisher's Exact Test 單尾檢定相同:

x <- matrix( c(33,20,14525,23996), ncol=2)
out <- fisher.test(x, alternative = "greater")
out$p.val = P[X ≥ 33]

	+	-
+	33	14558-33	14558
-	20	24016-56	24016
	53	38574-53	38574