we have several microarrays experiments, for which we have the list of differentially regulated genes. We analyzed the overlap for each of the pairs and now would like to know how significance are these overlaps.
I did it with the
phyper function this way:
set 1 mit 2
totalNumarrays = 21542 # total number of array probes DEgene_set1 = 1453 # differentially regulated genes of set 1 DEgene_set2 = 4987 # differentially regulated genes of set 2 overlap =481 # overlap between the two sets. Prob = phyper(overlap -1, DEgene_set1, totalNumarrays, DEgene_set2, lower.tail=FALSE, log.p = FALSE)
The same was done for set1 1 vs. 3 and 1 vs. 4 wth the same total amount of genes.
Now, my problem is, that sets 3 and 4 are from different technologies. They have different total number of array probes.well, my question is basically - does it matter?
Do I need to modify the formula to get the correct results?
I would appreciate any help