Hi Shirley, shirley zhang wrote: > Dear all, > > I posted my question a few days ago, but haven't receive any response > yet. Could anybody help me? Appreciate any hints and suggestions. You likely didn't get a response because you aren't really doing anything pertinent to Bioconductor (except possibly you are using microarrays, although you don't say). Anyway, both aov() and lme() are either part of base R, or a recommended package, so your question probably belongs on the R-help list. A word to the wise - LSMeans are an invention by the SAS people that tend to raise passions almost as much as type III sums of squares on R-help. You are probably better off using RSiteSearch("LSMeans") to find out what you want to know rather than asking directly. Best, Jim > > ============================== > > I'm working with a nested model (mixed). > > I have four factors: Patients, Tissue, sex, and tissue_stage. > > Totally I have 10 patients, for each patient, there are 2 tissues > (Cancer vs. Normal). > > I think Tissue and sex are fixed. Patient is nested in sex,Tissue is > nested in patient, and tissue_stage is nested in Tissue. > > > I tried aov and lme as the following, > > >>aov(gene ~ tissue + gender + patients%in%gender + stage%in%tissue >>lme(gene ~ tissue + gender, random = list(patients = ~1 , stage = ~ 1)) > > > > I got results from aov, but I got error message from lme which is > false convergence (8). so I could not compare the results of aov with > lme. > > Could anybody tell me whether I use the correct command? How can I get > LSMeans for Cancer vs. Normal in R ( I know it is easy in SAS)? > > Thanks, > > Shirley > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.