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workshop:2016:questions [2016/03/11 14:59] 65.114.233.215 [Questions/comments from Friday] |
workshop:2016:questions [2016/03/11 16:25] 65.114.233.215 [Questions/comments from Friday] |
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- | [[http://goo.gl/forms/ | + | Ask questions at the [[http://openmx.psyc.virginia.edu/forums|OpenMx forums]] and the [[http:// |
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??? 2. In her folder from Monday, Hermine Maes provided many different scripts, which is absolutely great! Is is possible to give some explanation to these scripts and in what they differ (except of ACE, ADE & SAT which is quite clear)? | ??? 2. In her folder from Monday, Hermine Maes provided many different scripts, which is absolutely great! Is is possible to give some explanation to these scripts and in what they differ (except of ACE, ADE & SAT which is quite clear)? | ||
!!! MN: Hermine' | !!! MN: Hermine' | ||
+ | |||
+ | Also, Hermine' | ||
+ | |||
+ | 1a- Analysis for 2 zygosity groups without any covariates and with an age covariate [a] | ||
+ | 1b- Analysis for 5 groups without any covariates and with age covariate [a] | ||
+ | |||
+ | 2- Each set includes a saturated model (SAT with sub models testing assumptions), | ||
+ | |||
+ | 3- Analyses for specific types of variables: continuous (c), binary (b), ordinal (o), mean/ | ||
+ | |||
+ | Two examples of the naming convention: | ||
+ | 1- The file called " | ||
+ | 2- The file called " | ||
??? 3. In classic Mx, we were able to include twin pairs with missing data. Can you clarify that we need to either drop twin pairs with any missing data or replace missing values with the mean? Are we not able to define a missing value and include that individual in the model? | ??? 3. In classic Mx, we were able to include twin pairs with missing data. Can you clarify that we need to either drop twin pairs with any missing data or replace missing values with the mean? Are we not able to define a missing value and include that individual in the model? | ||
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!!! For background, see [[http:// | !!! For background, see [[http:// | ||
- | Rob K. says: I would tentatively answer your second question with a " | + | Rob K. says: I would tentatively answer your second question with a " |
??? 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. |
+ | * If you're analyzing ordinal data, sometimes a status RED is unavoidable without changing some [[http:// | ||
+ | * Use different start values. | ||
+ | * Try a different optimizer. | ||
+ | * Reparameterize your MxModel. | ||
+ | * Use [[http:// | ||
+ | |||
+ | Trying different start values is the most important thing. | ||
??? 12. For Ben's presentation, | ??? 12. For Ben's presentation, | ||
- | !!! 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' | + | !!! Ben here - Here's the original LD Score MS: http://www.nature.com/ |
- | Ben here - Here' | + | ???13. What is the difference in interpretation between GCTA h2 estimates and LD score regression h2 estimates? |
- | here' | + | !!!MCK: I'll let Ben weigh in as well. But in essence, they should be two different ways of estimating |
- | here's the functional partitioning paper: http://www.nature.com/ | + | |
- | The Brainstorm stuff [neurology and psychiatry phenotypes] hasn't been submitted yet - should be soon and it'll be posted to bioRxiv soon - next couple of days. | + | ??? 14. @Sarah where can we find the full syntax of this morning's assumption testing (so the syntax with the right answers)? thanks! |
+ | !!! | ||
- | ??? 13. Can we have a short summary of how the estimates from GCTA and LD regression differ? | + | ??? 15. Where can researchers find publicly available twin data? |
- | !!! A few distinctions: | + | !!! 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). |
+ | |||
+ | As an aside, another publicly available resource towards developing harmonized measures of biomedical phenotypes is the PhenX toolbox (https:// | ||
- | 1) LD Score explicitly accounts for stratification through the incorporation of the intercept term in the regression analysis, which may yield substantial gaps between h^2 from GCTA and LD Score, in the event that stratification is contributing to variability. | ||
- | 2) GCTA is slightly more powerful, so has better standard errors than LD Score. | ||
- | 3)LD Score doesn' | ||
- | ??? 14. @Sarah where can we find the full syntax of this morning' | ||
- | !!! | ||
====== Questions/ | ====== Questions/ | ||