[R-sig-ME] residual variance estimates fixed to 1

Jake Westfall jake.a.westfall at gmail.com
Wed Jan 24 23:41:01 CET 2018

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.


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
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