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I am working with expression data from two different treatments(two gene lists) and would like to know if the overlap of genes between the gene lists is by chance or is it significant. Based on literature search it says use hypergeometric distribution - Phyper in R.
Here is my data
Total number of genes 26062
Gene list 1 - 1000
Gene list 2 - 1000
Overlap between two lists - 233
Now this is what I did
phyper(233, 1000, 26062, 1000, lower.tail = FALSE, log.p = FALSE)
and got the answer.
Can please some tell me how to interpret the output and also if I am doing it right,
So with that output how can I say that the overlap between two geen lists is by chance or if it is significant.