I'm trying to figure out the significance of the result of the intersection (venn) between two gene lists. While I often do this with lists from differential expression analyses originating from the same microarray platform, recently I've been using lists from different platforms (and also species). Applying the hypergeometric method for calculating the probability of an observed overlap makes sense to me when the intersecting lists originate from the same platform, but can it also be used when the source platforms are different?
Similar questions have been asked before- such as http://biostar.stackexchange.com/questions/15594/probability-of-gene-list-overlap and this one at crossvalidated but I didn't feel like they fully addressed this. Then again, I'm still having issues getting into the way that statisticians think.
I didn't even think previously that there would be possible issues with significance of list overlap if the lists had already been statistically filtered using reasonable cutoffs, so now I'd like to modify a web service we have to generate list intersections to also calculate these statistics.