IBG Wiki

User Tools

Site Tools

Trace:
workshop:2016:questions

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
workshop:2016:questions [2016/03/11 15:23]
65.114.233.215 [Questions/comments from Friday] 		workshop:2016:questions [2016/03/11 16:31] (current)
65.114.233.215
Line 2: Line 2:
  
 <note warning> <note warning>
-[[http://goo.gl/forms/8mhsgL2mXV|Ask questions with this Google form.]]+Ask questions at the [[http://openmx.psyc.virginia.edu/forums|OpenMx forums]] and the [[http://openmx.psyc.virginia.edu/forums/openmx-help/teaching-sem-using-openmx/boulder-workshop-2016|dedicated 2016 Workshop forum]] there.
 </note> </note>
  
Line 80: Line 80:
 !!! For background, see [[http://www.pnas.org/content/111/49/E5272|these]] [[http://www.pnas.org/content/112/40/E5452|papers]]. !!! For background, see [[http://www.pnas.org/content/111/49/E5272|these]] [[http://www.pnas.org/content/112/40/E5452|papers]].
  
-Rob K. says: I would tentatively answer your second question with a "yes," as long as you have a sample that is representative of the population of patients who meet diagnostic criteria for (whatever disorder).  Obviously, the generalizability of your results to the general population would be highly questionable.+Rob K. says: I would tentatively answer your second question with a "yes," as long as you have a sample that is representative of the population of patients who meet diagnostic criteria for (whatever disorder).  I'm not altogether sure, though.  Obviously, the generalizability of your results to the general population would be highly questionable.
  
 ??? 11. If we get a code Mx status RED, what do we need to do/consider (in general)? E.g., are our model estimates still reliable?  ??? 11. If we get a code Mx status RED, what do we need to do/consider (in general)? E.g., are our model estimates still reliable? 
 !!! Rob K. says:  Status RED means the optimizer is not certain it has found a minimum of the fitfunction.  So, no, your parameter estimates are probably not reliable, and the standard errors are even more suspect.  Status RED with code 6 (first-order conditions not met) is worse than with code 5 (second-order conditions not met).  You should always try to do //something// about status RED, for instance: !!! Rob K. says:  Status RED means the optimizer is not certain it has found a minimum of the fitfunction.  So, no, your parameter estimates are probably not reliable, and the standard errors are even more suspect.  Status RED with code 6 (first-order conditions not met) is worse than with code 5 (second-order conditions not met).  You should always try to do //something// about status RED, for instance:
-  * If you're analyzing ordinal data, sometimes a status RED is unavoidable without changing some [[http://openmx.psyc.virginia.edu/docs/OpenMx/latest/_static/Rdoc/mxOption.html|mxOptions]].+  * If you're analyzing ordinal data, sometimes a status RED is unavoidable without changing some [[http://openmx.psyc.virginia.edu/docs/OpenMx/latest/_static/Rdoc/mxOption.html|mxOptions]].  In fact, it's possible to get status RED with ordinal data even when the optimizer //has// found a minimum.
   * Use different start values.   * Use different start values.
   * Try a different optimizer.   * Try a different optimizer.
   * Reparameterize your MxModel.   * Reparameterize your MxModel.
   * Use [[http://openmx.psyc.virginia.edu/docs/OpenMx/latest/_static/Rdoc/mxTryHard.html|mxTryHard()]] or one of its wrapper functions.  Note that, by default, mxTryHard() prints to console the start values it used to find the best solution it found.  The idea is that you copy-paste those start values into your script, and assign them to your pre-mxRun() model, using [[http://openmx.psyc.virginia.edu/docs/OpenMx/latest/_static/Rdoc/omxSetParameters.html|omxSetParameters()]].   * Use [[http://openmx.psyc.virginia.edu/docs/OpenMx/latest/_static/Rdoc/mxTryHard.html|mxTryHard()]] or one of its wrapper functions.  Note that, by default, mxTryHard() prints to console the start values it used to find the best solution it found.  The idea is that you copy-paste those start values into your script, and assign them to your pre-mxRun() model, using [[http://openmx.psyc.virginia.edu/docs/OpenMx/latest/_static/Rdoc/omxSetParameters.html|omxSetParameters()]].
 +
 +Trying different start values is the most important thing.
  
 ??? 12. For Ben's presentation, where (papers, websites?) are the graphs on slides 17, 22, & 28 located? They are from published studies, yeah? ??? 12. For Ben's presentation, where (papers, websites?) are the graphs on slides 17, 22, & 28 located? They are from published studies, yeah?
-!!! MCK: I'll let Ben weigh in as well. But in essence, they should be two different ways of estimating the *same* parameter: SNP-heritability. I think that the differences in the literature are about what we'd expect given the SE's on the estimates. Ben - are there any systematic differences between the two?+!!! Ben here - Here's the original LD Score MS: http://www.nature.com/ng/journal/v47/n3/full/ng 
 + 
 +???13. What is the difference in interpretation between GCTA h2 estimates and LD score regression h2 estimates? 
 +!!!MCK: I'll let Ben weigh in as well. But in essence, they should be two different ways of estimating the *same* parameter: SNP-heritability. I think that the differences in the literature are about what we'd expect given the SE's on the estimates. Ben - are there any systematic differences between the two? 
 + 
 +??? 14. @Sarah where can we find the full syntax of this morning's assumption testing (so the syntax with the right answers)? thanks!  
 +!!! 
 + 
 +??? 15. Where can researchers find publicly available twin data? 
 +!!! One place a researcher can begin searching for publicly available data is the repository developed and managed by the Inter-university Consortium for Political and Social Research (ICPSR).  You can search for "twins" and datasets that have twin data collected and available for dissemination will be listed.  http://www.icpsr.umich.edu/ 
 + 
 +As an aside, another publicly available resource towards developing harmonized measures of biomedical phenotypes is the PhenX toolbox (https://www.phenxtoolkit.org/).  No data for analysis is available for download at this website, but it is good if you are thinking about study design of a project. 
 + 
 + 
 +MCK: Great question! Nick, Dorret, John?? Want to weight in?   
 +Sadly (I think), twin research has not kept up with whole-genome research, where sharing of data is not only the norm, but also mandatory (for NIH funding at least). Would be scientifically useful if the same were true of twin research! 
  
-Ben here - Here's the original LD Score MS: http://www.nature.com/ng/journal/v47/n3/full/ng 
  
 ====== Questions/comments from Thursday ====== ====== Questions/comments from Thursday ======
workshop/2016/questions.1457735016.txt.gz · Last modified: 2016/03/11 15:23 by 65.114.233.215

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International
CC Attribution-Noncommercial-Share Alike 4.0 International Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki