R help - Mar 2013 - how to do association study based on mixed linear model

Dear All:

I want to do association study based on mixed linear model,

My model not only includes serval fixed effects and random effects but
also incorporates some covariates such as "birth weight".
Otherwise, the size of the data are about 180 individuals and 12
variables and 60000 Fixed effect estimates

As asreml-R is not free ,is there any packages for my study?
I heard  nlme or lme4 but I'm not sure whether they could incorporate
covariates and what about their computational efficiency?

Thanks for you recommendation

Yao He
?????????????????????????
Master candidate in 2rd year
Department of Animal genetics & breeding
Room 436,College of Animial Science&Technology,
China Agriculture University,Beijing,100193
E-mail: yao.h.1988 at gmail.com
??????????????????????????

You need to do some reading and stop posting here. All your questions can
be answered by reading the appropriate Help pages of the packages you
mentioned  and associated references.

And what, pray tell, is "reml-R" and what does "is not free"
mean? (the
packages you mentioned are part of open source R and **are** "free"
under
their licensing conditions).

If you must post on this topic, post to the r-sig-mixed-models list.

-- Bert

On Tue, Mar 19, 2013 at 8:33 AM, Yao He <yao.h.1988@gmail.com> wrote:
> Dear All:
>
> I want to do association study based on mixed linear model,
>
> My model not only includes serval fixed effects and random effects but
> also incorporates some covariates such as "birth weight".
> Otherwise, the size of the data are about 180 individuals and 12
> variables and 60000 Fixed effect estimates
>
> As asreml-R is not free ,is there any packages for my study?
> I heard  nlme or lme4 but I'm not sure whether they could incorporate
> covariates and what about their computational efficiency?
>
> Thanks for you recommendation
>
> Yao He
> —————————————————————————
> Master candidate in 2rd year
> Department of Animal genetics & breeding
> Room 436,College of Animial Science&Technology,
> China Agriculture University,Beijing,100193
> E-mail: yao.h.1988@gmail.com
> ——————————————————————————
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

	[[alternative HTML version deleted]]

Yao He <yao.h.1988 <at> gmail.com> writes:
> 
> Dear All:
> 
> I want to do association study based on mixed linear model,
> 
> My model not only includes serval fixed effects and random effects but
> also incorporates some covariates such as "birth weight".
> Otherwise, the size of the data are about 180 individuals and 12
> variables and 60000 Fixed effect estimates
> 
> As asreml-R is not free ,is there any packages for my study?
> I heard  nlme or lme4 but I'm not sure whether they could incorporate
> covariates and what about their computational efficiency?
  I believe ASREML-R is free *for noncommercial use* (your address
is at a university, so you might qualify).

  It looks like Windows only, and you need a valid university
e-mail:

http://www.vsni.co.uk/software/free-to-use/teaching/asreml-teaching

  If that doesn't work, then lme4 might (although are you sure
you need 60K *fixed* effects?  Sounds like you need some kind
of penalized regression approach -- or maybe you're going to
do massive multiple comparisons correction??)  You should definitely
follow Bert Gunter's advice in this case and read some documentation
before asking a more focused question on the r-sig-mixed-models
list