Hi Margaret, Have a look at qqmath in the lattice package. ?qqmath Hank On Aug 16, 2007, at 2:45 AM, Margaret Gardiner-Garden wrote:
> 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 > > > > > > > [[alternative HTML version deleted]] > > <ATT00001> Dr. Hank Stevens, Associate Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ "E Pluribus Unum" If you send an attachment, please try to send it in a format anyone can read, such as PDF, text, Open Document Format, HTML, or RTF. Please try not to send me MS Word or PowerPoint attachments- Why? See: http://www.gnu.org/philosophy/no-word-attachments.html ______________________________________________ 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.