[R-sig-ME] Question on mixed model design to analyze microarray data

[Russ Lenth]

The lsmeans package can do the comparisons with control for each gene 
using something like this:

     lsmeans(fitted.model, trt.vs.ctrl ~ trt | gene, ref = 1)

... assuming that the control is the 1st lvel of treatment.

lsmeans does not do the overall F test of treatments at each gene. You 
need the multcomp package for that.

I have noticed that pbkrtest can give different df than SAS in cases 
where one or more variance components is estimated to be zero -- was 
that the case? When tghat happens, SAS pools the corresponding terms 
with residual error before getting the df.

Russ
-- 
Russell V. Lenth  -  Professor Emeritus
Department of Statistics and Actuarial Science
The University of Iowa  -  Iowa City, IA 52242  USA
Voice (319)335-0712 (Dept. office)  -  FAX (319)335-3017
russell-lenth at uiowa.edu  -  http://www.stat.uiowa.edu/~rlenth/