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
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