# [R] syntex about a nested mixed linear model

JongJoo Kim kimjj at email.arizona.edu
Thu Sep 2 23:46:31 CEST 2004

```I am a novice R user, and have been in trouble to get the right mixed
model syntax in microarray analyses.

There are three factors: Dye(2 levels), Temperature(3 levels) and
Array(3 for each Temperature with a total of 9 arrays). I want to treat
array as random, and to regard array variation different between
Temperatures.

So the model I want to seek is:

Y = Dye + Temp + Dye + Temp*Dye + Array(Temp) + Dye*Array(Temp).

For F tests of Dye and Dye*Temp, then denominator factor is
Dye*Array(Temp). For F test of Temp, then denominator factor is
Array(Temp).

I wrote this syntax to fit the above model by typing:

R2.0<-lme(dsnx.0 ~ temp+Dye+temp*Dye, random = list(
Dye*Array(Temp)=pdDiag(~-1+temp*Dye),  Arra=pdDiag(~-1+temp) ) ).

But there is syntax error message.
To obtain one solution, I typed

>int.dye<-interaction(Dye,temp:Arra,drop=T)
which created another factor, int.dye for 'Dye*Array(Temp)', and I
typed:

>R2.0<-lme(dsnx.0 ~ temp+Dye+temp*Dye, random = list(
int.dye=pdDiag(~-1+temp*Dye),  Arra=pdDiag(~-1+temp) ) )

It worked but the degree of freedom for int.dye is 12 instead of 6 <=
(2-1)*3*(3-1).

Could you solve the syntax to fit the right model for this nexted mixed
model?
Thanks so much for your guidance.
Jong
--
JongJoo Kim, Ph.D.

243 Shantz Building
Department of Animal Science
University of Arizona
Tucson, AZ 85721
Tel) 520-621-9757
Fax) 520-621-9435
kimjj at email.aizona.edu

```