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

Lindner, Melanie melanie.lindner at helsinki.fi
Wed Jan 24 19:02:27 CET 2018

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,

	[[alternative HTML version deleted]]

More information about the R-sig-mixed-models mailing list