Estimate lambda

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Estimate lambda

Postby hakosalo » Fri Oct 14, 2011 8:08 am

I am running to this warning all the time with many of my analysis if I try to do association analysis
> Assoc1<-qtscore(pheno,, trait="binomial")
Warning message:
In qtscore(pheno,, trait = "binomial") : z2 lambda < 1, set to 1

In this case my is not human data, but canine. Does that make a difference for this estimation? Does this matter anyway? I can run "polygenic" for this data set anyway, eventhough quite often if I have trait="binomial" it gives BAD CONVERGENCE which is kind of expected? If I have quantitative trait and BAD CONVERGENCE what should I do? (sample sizes are normally 20-60 cases with similar number of controls)

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Re: Estimate lambda

Postby MariaG » Wed Oct 19, 2011 2:52 pm

Here is the additional message from the same author (hakosalo):

hakosalo wrote:Hi.
I have this type of error message appearing over and over again (my data is not human, its canine)

"Testassoc<-qtscore(pheno,, trait="binomial")
Warning message:
In qtscore(pheno,, trait = "binomial") : z2 lambda < 1, set to 1"

Why is it in almost every data set I analyze give this message, and does this matter? Sample size is normally everything between 20-60 cases + same amount of controls.

Also, when I try to estimate the possible polygenic effect i get :
MyPol<-polygenic(pheno,, kin=Bkin, trait="binomial")
LM estimates of fixed parameters:
[1] -0.09531018
iteration = 0
[1] 0 0 0


and so on all the way to the message :

[1] 0.495997
fixed effect betas changed to FGLS-betas for re-estimation

*** !!!BAD!!! convergence indicated by FGLS ***

Now, is this because I have binary trait or what?

Anyway I try to test also mixed model , I get the same lamda message:

> MixTest<-qtscore(MyPol$pgres,
Warning message:
In qtscore(MyPol$pgres, belgit) : z2 lambda < 1, set to 1

Why doesn't the program accept lambda which is smaller than one? Why am I getting it all the time? The data should be ok. Does it make a difference that I don't have human, but canine data?

Thanks for your answers!


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Posts: 263
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Re: Estimate lambda

Postby yurii » Sat Oct 29, 2011 12:18 pm

Re: z1<1, see

With polygenic, do not use "binomial" option -- see


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