Question: Calculation of 2 sided p value from Monte Carlo simulation with frequency parameters?
gravatar for hs.lansdell
3 months ago by
hs.lansdell0 wrote:


I'm hoping for some logic checks on a simulations set I've been working on. I know the theory and equations for a two sided p value as derived from normal distributions and from Monte Carlo simulations. My issue more is my test statistic.

To construct my monte carlo matrix, I took ~13,000 genes and randomly selected 402 genes 10,000 times. Reason being that I have a list of 402 genes of interest that I am mapping the miRs to, and I am observing if they occur more in this set more than 402 random genes. So after I have the 10,000 simulations, I have columns of 402 genes each, those are then mapped to the miRs that target them, and I count how many times those miRs occurs across those 402 genes.

So my final product is a matrix where each column representing first the frequency of the miRs in the set of interest then in the simulations. Rows are the individual miRs.


         mygene_freq   sim1      sim2   etc...
mir1        5           3         4
mir2        2           2         1
mir3        1           3         3

My question is, since the number of miRs in each element is a calculated probability from the Monte Carlo, is this my test statistic? I want to compare whether the observed frequency of mir1 in mygene set is statistically significant from the 10,000 simulations for example.

Thank you!

ADD COMMENTlink modified 29 days ago by Biostar ♦♦ 20 • written 3 months ago by hs.lansdell0

I don't see where you're going with this. What is the question you're trying to address ? It looks to me that you're asking whether your 402 genes are enriched in miRNAs targets compared to a random set of genes. Why can't a Fisher's exact test (or equivalent) not answer that question ?

ADD REPLYlink modified 3 months ago • written 3 months ago by Jean-Karim Heriche15k
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