Imagine an organism that has 10 genes, and a pathway that is composed of all those genes. You run an experiment, test all 10 genes, and find 3 genes that are differentially expressed and belong to that pathway. What would be the p-value for enrichment on that pathway according to ORA?
I didn't understand this question and my teacher gave me the comment:
Please either:
i) use the formula for hypergeometric test;
ii) or consider: How probable it is to get at least as extreme of a result under H0 (no upregulation), if all the genes are in the pathway?
When looking up the hypergeometric test online I am unsure as to what N, n, K and k are in my case. I would assume that both N and n = 10 and K and k = 3. This however leads to a p-value of 1 which I do not believe is correct.
All help is appreciated!
