Closed:Calculating the hypergeometric value for overlap of two lists of genes
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5.9 years ago
Za ▴ 140

Hi,

I have a list of genes with their biological score like below

       gene       score
    G0295603 0.9922432
    G0295719 0.9917077
    G0282307 0.9876919
    G0269672 0.9862853
    G0284895 0.9853162
    G0274031 0.9803622
    >

In this list, number of genes with score> 0.5 = 2475 and number of genes with score < 0.5 =2391

If I extract 422 genes from this list, 226 genes have score > 0.5

I want to know if these 226 genes have score > 0.5 by chance or no, so

> phyper(226-1,2475,2391,422,lower.tail = FALSE)
[1] 0.1342791

Does this means, yes these 226 genes only by chance have score > 0.5 because 0.1342791 is greater than 0.05????

Thank you

R gene RNA-Seq hypergeometric • 160 views
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