Here there are two list of genes. One is a set of genes (about 500 genes), the other is all the genes (about 20k). And each gene has a number meaning the number of genes interacted with it. To compare whether or not they are different concerning the number of interacted genes, which kind of test should be used? Thank you.
A = c(4, 5, 40, 3, 0, 0) #length(A)=500
B = c(1,2,0,0,0,43,65,...) #length(B)=20000
Genes from A are also from B.
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written
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Zhilong Jia
All normal approximations are out-of-bounds in this setting. I think your best bet is Kruskal-Wallis.
However, I'd temper your enthusiasm for the very low p-values it might return, as there are some serious acquisition biases in interactome data (and KW provides no way to control for them)
A <- rpois(50, 10)
B <- rpois(50, 100)
kruskal.test(list(A, B))
Yes, there are biases in interactome data, esp. lots of 0s. Any other test which could be used? Thank you.
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written
by
Zhilong Jia
It should work.
Yes, it works. Thank you.
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