Command tutorial

[mcri...@gmail.com]

I am trying to access to the command tutoria (https://psychgen.u.hpc.mssm.edu/dnenrich/command_tutorial.shtml) in your website and it is completely impossible. I would appreciate if anyone could sent me the dnenrich command tutorial
Thank you very much in advance
Best regards
Cristina

https://psychgen.u.hpc.mssm.edu/dnenrich/

[Menachem Fromer]

OK, this should all be working now - I fixed some transient errors.

Enjoy!

Menachem

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[mcri...@gmail.com]

We've been trying to run Dnenrich in different data sets. We would like to answer you some questions regarding the p-value results. In some cases, the p-value is around 9,999e-005 which doesn't make any sense. Therefore, we have many analysis which have resulted in the same p-value. We have increased the number of permutation to 1000000 but the results have only changed to  9,999e-007. We would appreciate any help regarding this issue. We are not completely sure about this.
Thank you very much
Best regards
Cristina 

[Menachem Fromer]

Since dnenrich uses permutation, the p-value (under the dnenrich null model) of the particular event you are testing is less than 10^-4 and even 10^-6. You can either report that p < 10^-6, or keep increasing the number of permutations until it gives you a better estimate that is not the lowest possible for that number of permutations. Of course, the latter may require you to wait for a while. You could however manually parallelize it by running 100 runs of 10^6 permutations each (10^8 permutations in total) and then:

1. multiply each run’s p-value by (10^6 + 1)

2. Subtract 1 from each result in 1

3. Add up all the results from step 2

4. Add 1 to the sum of events from step 3

5. Divide the result from 4 by (10^8 + 1)

Note that the whole thing here with 1 (adding or subtracting) is because dnenrich always counts the original observation of the event in question once in the numerator and once in the denominator.

To view this discussion on the web visit https://groups.google.com/d/msgid/dnenrich-users/833f65fb-0767-46bb-92ff-ac664ce5de25%40googlegroups.com.