Behavioral Genetics Models
JuanJMV
Joined: 07/20/2016
Problem to get the genetic correlations
Hi everyone,
I have fitted a 4-variate model and I have fixed A to 0 for one of these phenotypes. The model fits OK but I am struggled to obtain the genetic correlations.
This is the output from the model but as one of the A parameters is fixed to 0 I get these results:
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liagym1
Joined: 11/06/2019
ACE with moderator- warning in output
I'm running an ACE with moderator script, on Mx. When I drop one of the parameters (U), I receive this message-
Mx starting optimization; number of parameters = 7
*** WARNING! ***
I am not sure I have found a solution that satisfies
Kuhn-Tucker conditions for a minimum.
NAG's IFAIL parameter is 6
Looks like I got stuck here. Check the following:
1. The model is correctly specified
2. Starting values are good
3. You are not already at the solution
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lemire
Joined: 12/13/2019
Genetic correlation: two ways, two different estimates
Hi,
I implemented two ways of calculating the genetic correlation between two phenotypes, estimated from twins (direct model of rg between A1 and A2, and Cholesky).
My two implementations are based on the path diagrams from H.H. Maes' slides 18 and 53 found at
https://vipbg.vcu.edu/media/course/HGEN619_2015/BivariateGeneticAnalysis2.pdf
I do not get the same estimates between the two methods (-0.26 vs 0.51). Below is the code with the reproducible fake data and results. The code is also attached.
ReddyM
Joined: 10/02/2019
Ordered quantile normalization
Can i use ordered quantile normalization, to normalize a dataset for univariate ACE model? I think not, but if i could, that would be really good.
Thanks in advance!
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diana
Joined: 04/17/2019
How to fix the genetic correlation larger than 1
Hi everyone, I am fitting a bivariate ACE model and I am very confused about the Ra (genetic correlation of two traits) that is larger than 1. Since Ra is a correlation coefficient, it should range from -1 to 1, am I right? I don't know how to explain this result.
In the ACE model, Ra=1.37 ,Rc=-0.04, Re=0.22.
Then I fitted ADE model, Ra=0.07, Rd=NA, Re=0.22.
The results of the goodness-of-fit test between saturated model and ACE or ADE are as follows.
qingwen
Joined: 08/15/2019
CI is confusing
I fit a nuclear twin family model. AE model is the best. However, the CI of e makes me confused. Here are the output in free parameters and CI details section. The CI details looks strange, ranging from 0 to 2.053589e+06.
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liagym1
Joined: 11/06/2019
ACE with moderator-help interpreting results
I am using regular Mx (unfortunatly i cannot find an active forum), and would like to clarify the meanings of the output received after running in an ACE with an ordinal moderator script.
1. Are the estimates of T,U,V the moderated components? (often denoted by betas)
2. If the estimate for a certain parameter is not zero, yet the CI contains zero- does this imply that this component is not significant?
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liagym1
Joined: 11/06/2019
Error in output
I am trying to run an ACE with moderator script, and this is the error I received in the output. What changes should i make in my data?
Error found in rectangular data; record number 1 :
1004 -999 -999 -999 -999 -999
We have a problem whose error code is 176
and which I ran across at line number 38
of your input script
RE FILE=AGE11DATA.DAT
~~~
An error has occurred while reading a rectangular file
Make sure that you *don't* have a FORMAT at the beginning
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ReddyM
Joined: 10/02/2019
Difference between optimizers
In my twin model i calculate Rmz and Rdz from the saturated model, however when i run it (i run it on several variables) for a few variables CSOLNP fails to calculate confidence intervals, while SLSQP does caculate all. Is there a particular reason for this? Should i be concerned by this, or just use slsqp for the cases csolnp fails?
Here is the sat part, if it helps:
#sat model, rmz, rdz:
PathMZ <- mxMatrix("Lower",nrow = 2,ncol = 2,free = TRUE,values=starting_value_pathcoeff,name = "PathMZ")#cholesky for pos definitness
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lior abramson
Joined: 07/21/2017
direct comparison between traits' heritability with no raw data
Dear forum
I am trying to conduct a meta-analysis on the heritability of two traits that are different, yet related (I found six studies in which the twins were measured in both traits).
From what I know, in order to directly compare between the two traits heritability, I need to enter them in the same model, and for that, I need either the raw data or the full correlation matrix (and I have neither).