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

[Lindner, Melanie]

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



	[[alternative HTML version deleted]]