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Bayesian network analysis on large dataset (Read 3675 times)
Catherine Macken
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Bayesian network analysis on large dataset
Jan 24th, 2013 at 8:19am
 
I am a VERY newbie HyPhy user, and so perhaps this is plunging in the deep end too quickly. However, I would like to infer a Bayesian network for a dataset that exceeds the limits allowed by datamonkey.org. Is there a batch file available for this process? Or perhaps a command line file? (I have a good tree already.) I use a Mac G5 desktop, and have installed HyPhy, which recognizes that my desktop has multiple processors. I also may have access to a cluster that uses MPI, on which I may be able to install and run HyPhy.  I would appreciate your suggestions.
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Sergei
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Re: Bayesian network analysis on large dataset
Reply #1 - Jan 24th, 2013 at 8:32am
 
Hi Catherine,

I would suggest that you refer to Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login section 1.8 which has a tutorial on how to run BGM analyses in HyPhy.
Also make sure you get a fairly recent HyPhy version -- there was a period when HyPhy BGM files were broken in the distribution.

Sergei
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Catherine Macken
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Re: Bayesian network analysis on large dataset
Reply #2 - Jan 25th, 2013 at 7:57am
 
Thanks.  I look forward to my adventure.  Catherine
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Art F. Poon
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Re: Bayesian network analysis on large dataset
Reply #3 - May 16th, 2013 at 12:10am
 
Hi Catherine,
Sorry I haven't replied to your post - my account on the board got deleted and I had a lot of trouble trying to get a new one set up.  I wrote the Bayesian network code and would be happy to help you with your analysis.
Cheers,
- Art.
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Jason
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Re: Bayesian network analysis on large dataset
Reply #4 - Sep 21st, 2013 at 6:52am
 
Hello Art and Sergei,

I too am trying to run a BGM analysis. I downloaded and started using HyPhy only last week and so my version should be the most up-to-date. I have been going through the Epistasis section 1.8 in  Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login to get a feel for the tool. I have used all the default parameter settings (and tried some others) and get the following error after choosing ancestral resampling (both yes and no):

Error: The left hand side expression does not contain an object reference in the following context: 'BGM gen_bgm=<ERROR HERE>(discreteNodes.continuou'

Function call stack
1 : BGM gen_bgm=(discreteNodes,continuousNodes)

Any help/guidance you can give would be greatly appreciated.

Thanks,
Jason
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daven
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Re: Bayesian network analysis on large dataset
Reply #5 - Oct 1st, 2013 at 9:26pm
 
Hi all,
I am also using the most recent hyphy-2.2 version and I get exactly the same error message as Jason, both with an installation of the program on a linux server and on my own macbook pro.

Any help will be greatly appreciated, I have tried a thousand things and always ended up getting the same error message.

Thanks in advance Smiley
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