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error messages in directionalREL.bf (Read 9344 times)
Kohei
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Re: error messages in directionalREL.bf
Reply #15 - Jul 4th, 2010 at 6:09pm
 
Second, I re-ran DirectionalREL.bf with REV model; it took about 33 hours. Now amino acid sites 51, 125, 236, and 242 are selected; these sites are "more preferable" in that they correspond with variable regions known in the gene, which encodes viral outer capsid. However, I still find so many N/A in the resulted xxx_AA_bysite.csv file. Does this situation occur when the variation (the number of substitutions) in the alignment is too small ?
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Sergei
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Re: error messages in directionalREL.bf
Reply #16 - Jul 6th, 2010 at 12:07pm
 
Hi Kohei,

N/As are normal. As described in the DEPS manuscript, the stage consists of two steps:

1). For each target residue, a p-value is computed to determine if there are ANY sites (proportion > 0) directionally evolving towards that residue. That's the top row of the spreadsheet that you attached.

2). For those residues which show significant p-values (after a multiple test correction), Bayes Factors are computed

N/A simply means that there was no need to compute Bayes Factors for that particular residue/site pair because the LRT test was not significant.

Sergei
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Kohei
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Re: error messages in directionalREL.bf
Reply #17 - Jul 11th, 2010 at 9:21am
 
Dear Sergei,

Thank you for your kind reply.
I should have read the DEPS manuscript in detail; now I am trying to do so. I hope that I can obtain meaningful information.

Kohei
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