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GA-Branch - model averaged probabilities output (Read 2967 times)
Daryn
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GA-Branch - model averaged probabilities output
May 11th, 2010 at 12:33pm
 
Sorry to bother you, but I have a quick question concerning the “model averaged probabilities that any two branches have the same dN/dS” output generated by GA-Branch. Can these probabilities be taken as p-values where anything <5% would be considered a significant difference and if so, should a Bonferroni correction for multiple comparisons be used prior to determining which lineages are significantly different?

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Daryn
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Sergei
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Re: GA-Branch - model averaged probabilities output
Reply #1 - May 12th, 2010 at 6:36pm
 
Hi Daryn,

The values reported by GABranch are NOT p-values; the closest analogy are posterior probabilities (or something like 1-p), but even then GA only approximates those under some assumptions. If the value is low for a pair of branches, you can say that the models with high c-AIC scores (credible set) assign different rates to these branches. However, I would just leave it at that -- do not try to interpret those as p-values (because those imply a hypothesis test which is not performed here), and definitely do not use the Bonferroni correction.

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Sergei
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Daryn
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Re: GA-Branch - model averaged probabilities output
Reply #2 - May 12th, 2010 at 7:02pm
 
Thanks!
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