residual variance estimates fixed to 1

-----Original Message-----
From: R-sig-mixed-models [mailto:r-sig-mixed-models-bounces at r-
project.org] On Behalf Of Jake Westfall
Sent: Wednesday, 24 January, 2018 23:41
To: Lindner, Melanie
Cc: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] residual variance estimates fixed to 1

Hi Melanie,

As far as I know, lmer never fixes the residual variance to 1 or any
other
value, and in fact this isn't even possible to do with lmer (at least not
without resorting to add-on packages). My guess is that in your loop you
accidentally grabbed the wrong field, not the variable giving the
residual
variance estimate. If you give us a sample of the code you used, we could
help figure out what happened.

Jake

On Wed, Jan 24, 2018 at 12:02 PM, Lindner, Melanie <
melanie.lindner at helsinki.fi> wrote:

Hi again,

I use lme4 to model methylation count data. I specify my response as
cbind(methylation count, unmethylation count) and use the argument
family=binomial.
In my data set I have count information for 500,000 CpG sites over 64
samples (so, each sample contains count information for all 500,000

sites).

32 per treatment group. I model each site separately to see if there is

a

significant difference between the treatments and therefore use a loop.
Since I cannot look at the summary of each site, I saved different
estimates from the loop and recognised that the residual standard

deviation

is always 1. To evaluate the model fit, I would like to understand why

the

residual variance is fixed to one. It would be great if someone can

tell me

where to find information on that.

Thanks in advance,
Melanie