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 [EMAIL PROTECTED] ______________________________________________ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
