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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

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I found a possible solution, apparently GSEA would be better than a simply hypergeometric test.

More info: http://software.broadinstitute.org/gsea/index.jsp

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  • $\begingroup$ Isn't GSEA commonly done by a simple hyper-geometric test? $\endgroup$
    – Scholar
    Jan 17, 2019 at 19:39

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