[R-sig-ME] Question on mixed model design to analyze microarray data
Russ Lenth
russell-lenth at uiowa.edu
Mon Jul 1 17:54:05 CEST 2013
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/
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