I have to select the background for an hypergeometric test that I have to perform. The problem is as follow:
I have a list of genes differentially expressed in cell B between "control vs treatment". I want to see if there is an overlap between the genes up regulated in this experiment with genes that are Up regulated between cell A vs cell B. As you can notice the cell B is different from the cell A and I am wondering if there is a suitable strategy to handle this problem.
Thanks in advance for any suggestion