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. 

 

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.  I apologise in advance for the lack of subscripts.

 

 logit P(yij=1) = â0 + Ui + â1Patholij where Ui~N(0, óu2),

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 (or even for any 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

 

 


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