Dear all,
I was just trying to analyse some microarray gene expression data using mixed models in R.
Based on the SAS code given here
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_hpmixed_sect035.htm
   proc hpmixed data=microarray;
      class marray dye trt gene pin dip;
      model log2i = dye trt gene dye*gene trt*gene pin;
      random marray marray*gene dip(marray) pin*marray;
      test trt;
   run;

I wanted to try to run the equivalent model in R using lmer and then test significance using lmerTest and/or lsmeans. Am I correct that the correct syntax would be
lmer(log2i~dye+trt+gene+dye:gene+trt:gene+pin+(1|marray)+(gene|marray)+(1|marray/dip)+(pin|marray), data=microarray)
(gene has about 10 000 levels and marray 10, would this run in lmer?)

Also, would it be possible in any way to allow variances across treatment (trt) groups to be unequal? Or is that only possible in nlme/lme? (but that wouldn't allow for such complex random effect designs, right?)

Cheers,
Tom





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