I have compared 1370 genes which are obtained from chip seq analysis and 652 number of genes which are differentially regulated genes obtained by analyzing affymetrix 430.2.0 mouse array. When i intersect list both these lists of genes i got 37 genes common.
Now i would like to calculate what is the significance of this over lap. I was thinking to use phyper in R but this requires total number of genes here i am confused which number to give . Should i give total number of probes from affymetrix chip or should i give whole mouse genome number from chip seq data..
One more question can anybody suggest some ways how exactly to perfom this significance test in R.