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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Datamonkey Server >> Datamonkey feedback >> Site with very high dN not significant in FEL and FUBAR http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1385734643 Message started by jhughes on Nov 29^th, 2013 at 6:17am

Title: Site with very high dN not significant in FEL and FUBAR
Post by jhughes on Nov 29^th, 2013 at 6:17am

Hi,

I have been looking at the output from FEL and FUBAR on a set of analyses from different genes. In one gene, I have a site with a dN > 6 and dS = 0 which IS NOT significant. In another gene, the highest dN I have is 3.78 and dS = 0 and this IS significant for both FUBAR and REL.
There are the same number of sequences for both genes so I dont think it is a samples size issue.
I would be really grateful if someone could explain why this may be.

Kind regards,
Joseph

Title: Re: Site with very high dN not significant in FEL and FUBAR
Post by Sergei on Nov 29^th, 2013 at 11:37am

Hi Joseph,

You should NEVER look at point estimates for guidance, because they give you no indication of variance. For example, your site with dN = 6 and dS = 0 could have only one non-synonymous substitution along a short branch, and the LRT (which accounts for variance) is not significant, e.g. because dN = 6 +/- 3 and dS = 0 +/- 5 (hypothetically speaking).

The number of sequences is only one component of the "effective" sample size: FUBAR and FEL both derive signal from substitutions, i.e. if one site has more substitutions (roughly speaking), it will have a more precise estimate of dN and dS.

Sergei

Title: Re: Site with very high dN not significant in FEL and FUBAR
Post by jhughes on Dec 2^nd, 2013 at 1:01am

Hi Sergei,

Thanks for the quick response, it actually makes total sense and was quite a silly question now that I think of it.

Cheers,
Joseph