Calculation of 2 sided p value from Monte Carlo simulation with frequency parameters?
0
0
Entering edit mode
4.2 years ago

Hello,

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.

i.e

         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!

R miRs Monte-Carlo Hypothesis Testings • 1.6k views
ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 969 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6