Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
Bayesian network analysis on large dataset (Read 4412 times)
Catherine Macken
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 9
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.
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
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
Back to top
 

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
WWW WWW  
IP Logged
 
Catherine Macken
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 9
Re: Bayesian network analysis on large dataset
Reply #2 - Jan 25th, 2013 at 7:57am
 
Thanks.  I look forward to my adventure.  Catherine
Back to top
 
 
IP Logged
 
Art F. Poon
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 3
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.
Back to top
 
 
IP Logged
 
Jason
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 1
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
Back to top
 
 
IP Logged
 
daven
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 5
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
Back to top
 
 
IP Logged