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Methodology Questions >> How to >> F_st compartmentalization permutation result http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1376378250 Message started by eunok on Aug 13th, 2013 at 12:17am |
Title: F_st compartmentalization permutation result Post by eunok on Aug 13th, 2013 at 12:17am
Hi,
I am currently doing Fst compartmentalization analysis with permutation test. I set permutation as 1000 and I am getting some permutation results of 0. How do I correct permutation result of 0? Is there a way to increase decimal places in this analysis? Thank you! Eunok |
Title: Re: F_st compartmentalization permutation result Post by Sergei on Aug 13th, 2013 at 10:07am
Hi Eunok,
Sorry, I don't quite understand your question. Can you paste the text output by F_st and point out to the zeros that are suspect? Sergei |
Title: Re: F_st compartmentalization permutation result Post by eunok on Aug 15th, 2013 at 2:10am
Hi Sergie,
So, I used F_ST.bf from the standard analysis. For distance computation, I chose Full likelihood and then I loaded DNA sequence data. Then I entered regular expressions to define 2 clades. For the standard standard substitution model, I chose CUSTOM so I could type "012345" for GTR. After selecting several parameters, I did permutation test (1000 permutations). Then, I obtained "zero" for Prob (Random F_ST> Observed F_ST) like below: Prob {Random F_ST > Observed F_ST} Hudson, Slatkin and Maddison : 0 Slatkin : 0 Hudson, Boos and Kaplan : 0 Hudson, S_nn : 0 My question is whether the result above is indeed 0. (Or is it because of small number of decimal places? If it is so, how can I increase the number of decimal places?) I hope my question makes sense......... Eunok |
Title: Re: F_st compartmentalization permutation result Post by Sergei on Aug 16th, 2013 at 10:36am
Hi Eunok,
OK, I understand. The zero you see is actually a zero (i.e. no decimal places). A general rule of thumb for you to estimate p-values based on permutations when there are exactly 0 / N replicates that beat the observed value, is to say that P <= 1/(N+1) [because in the worst case, the very next replicate might have beat the observed value]. Hence, you can report the p-value as <=1/1001 Sergei |
Title: Re: F_st compartmentalization permutation result Post by eunok on Aug 29th, 2013 at 3:56am
Thank you so much!!!! :)
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