Hi, I was wondering if I might be able to ask some advice about doing residual plots for the lmer function in the lme4 package.
(Apologies to anyone who has received this message twice. I have had problems with embedded text.) Our group's aim is to find if the expression staining of a particular gene in a sample (or "core") is related to the pathology of the core. To do this, we used the lmer function to perform a logistic mixed model below. logit P(yij=1) = beta0 + Ui + beta1Patholij where Ui~N(0, sigmaU2), i indexes patient, j indexes measurement, Pathol is an indicator variable (0,1) for benign epithelium versus cancer and yij is the staining indicator (0,1) for each core where yij equals 1 if the core stains positive and 0 otherwise. (I have inserted some example R code at the end of this message) I was wondering if you knew how I could test that the errors Ui are normally distributed in my fit. I am not familiar with how to do residual plots for a mixed logistic regression. Any advice would be greatly appreciated! Thanks and Regards Marg Example code: lmer(Intensity.over2.hyp.canc~Pathology + (1|Patient.ID), data= HSD17beta4.hyp.canc, family="binomial", na.action="na.omit") #Family: binomial(logit link) # AIC BIC logLik deviance # 414.1101 431.4147 -203.0550 406.1101 #Random effects: # Groups Name Variance Std.Dev. # Patient.ID (Intercept) 4.9558 2.2262 # of obs: 559, groups: Patient.ID, 177 #Estimated scale (compare to 1) 0.6782544 #Fixed effects: # Estimate Std. Error z value Pr(>|z|) #(Intercept) -2.05734 0.24881 -8.2686 < 2.2e-16 *** #PathologyHyperplasia -1.76627 0.44909 -3.9330 8.389e-05 *** NB. Intensity.over2.hyp.canc is the staining of the core (ie 0 or 1) Pathology is Hyperplasia or Cancer Dr Margaret Gardiner-Garden Garvan Institute of Medical Research 384 Victoria Street Darlinghurst Sydney NSW 2010 Australia Phone: 61 2 9295 8348 Fax: 61 2 9295 8321 [[alternative HTML version deleted]] ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.