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missing "Additional Information" column (Read 3650 times)

ben

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missing "Additional Information" column
Oct 29^th, 2008 at 10:27am

Dear Dr. Sergei Kosakovsky Pond,

I have two questions when analysing data on DataMonkey server:

(1). I run FEL/IFEL on DataMonkey server. But, "Addditional Information" column is missing on the positive selected sites table (the results page). Browsers I used are IE 7.0 and Safari

(2). How to choose P values : 0.05? (based on the paper "Adaption to Different Human Populations by HIV-1 Revealed by codon-Based Analyses")

Thanks!

Ben

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Sergei

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Re: missing "Additional Information" column
Reply #1 - Oct 29^th, 2008 at 2:07pm

Dear Ben,

It is not explicitly documented, but you need to have SLAC results for the additional information column to be generated; run SLAC first (to get ancestral sequences and such) and then FEL/IFEL. I will update the documentation to reflect this - thanks for pointing out this issue.

As far as p-values go: use 0.05 if you have > 50-70 sequences and 0.1 for fewer sequences. FEL/IFEL are conservative for smaller alignments so the nominal value of p=0.1 will actually result in lower false positives; at least that's the case in all the simulations we have done.

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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ben

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Re: missing "Additional Information" column
Reply #2 - Oct 30^th, 2008 at 7:26am

Dear Sergei,

Thank you very much! I will do it as you suggested!

One more question:

I want to compare two populations in terms of positive selection sites. Based on your paper "Adaptation to different human populations by HIV-1 revealved by codon-based analysis", you identified six codons in RT (82, 98, 165, 177, 196, and 202) as selected differentially in the two populations at p< 0.05 (see Table 2). my questoin is the calculation of "Different" on table 2 can be done on DataMonkey server? If yes, how to... If not, any suggestion?

Thanks!

Ben

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ben

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Re: missing "Additional Information" column
Reply #3 - Nov 1^st, 2008 at 11:17am

Dear Sergei,

I am still waiting for your response! I have two populations with 70 sequences for each one. I try to test if these two populations are selected differentially at P < 0.05. Can I do this on DataMonkey server. If not, what is suggestion?

In fact, I check PyPhy package, and find "compareSelectivePressureIVL.bf" under a standard analysis. But, I can't find instruction for how to do it!

Thanks!

Ben

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: missing "Additional Information" column Reply #4 - Nov 3^rd, 2008 at 6:48pm Dear Ben, Datamonkey.org does not handle the comparison analysis, but HyPhy does. Please examine section 2.7.1 of Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to Login for detailed instructions of how to do this. Best, Sergei
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ben YaBB Newbies Offline Feed your monkey! Posts: 6	Re: missing "Additional Information" column Reply #5 - Nov 5^th, 2008 at 12:21pm thanks Gergei! Ben
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