Microarray Analysis Statistics Question

Question

[perpetualpeace1]

Here's a (simplified) microarray analysis question. I could answer it by running permutations on the data, but I'm sure that there's an analytical method of answering the question that I just don't know. Any help?

In 5 different experiments with a 10,000 gene microarray, some number of genes were up-regulated at a 2-fold cutoff in each experiment (let's say 200, 300, 500, 700, and 1000 genes). 40 genes were up-regulated at a 2-fold cutoff in 5 out of 5 experiment, and 200 genes were up-regulated at a 2-fold cutoff in 4 or more experiments. Are those numbers significantly more than expected by chance?

Answer 1

[seidel]

I think you would use the hypergeometric distribution to assess the significance of overlap between two experiments, and then for more experiments would probably multiply the p-values (sort of like adding in more dice to a dice role). Since every array has the same 10,000 gene universe, you can calculate the significance of drawing the same set of genes between arrays in a given sampling (i.e. the set of genes called at a 2-fold cutoff). This question is very similar to one that was asked before. (though some people were confused about whether it was one experiment with 5 replicates, or 5 experiments, but like your question, it was actually 5 experiments).