[BioC] Interaction contrasts with RCBD with replicates

[Daniel [guest]]

Dear all,

I have a RCBD with three treatment levels and two blocks.  Within each block, I have 5 replicates for each treatment (that is, my block size is 15, 5 for each trt level).  

I am aware that since I have replicates within the blocks, the denominator for the treatment is supposed to be the treatment by block interaction.  

However, the person who I am analyzing the data for is interested in comparing the interaction (block*trt) and I am not quite certain how to setup the model statement in lmFit in this case, so that I can eventually test the interaction.

Does the code below fit the model and tests using the correct residuals (i.e. TRT*Block for TRT and Block, and sqrt(MSE) for TRT*Block)?

design <- model.matrix(~ 0+TRT*Block, pheno.Data)
correl=duplicateCorrelation(eset, design,block=Block)
fit <- lmFit(eset,design,block=Block,cor = correl$consensus)

I sincerely appreciate any help I can get.

Thanks,

Daniel

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] gcrma_2.28.0        BiocInstaller_1.4.6 car_2.0-12         
[4] nnet_7.3-1          MASS_7.3-18         affy_1.34.0        
[7] Biobase_2.16.0      BiocGenerics_0.2.0  limma_3.12.1       

loaded via a namespace (and not attached):
[1] affyio_1.24.0         Biostrings_2.24.1     IRanges_1.14.3       
[4] preprocessCore_1.18.0 splines_2.15.0        stats4_2.15.0        
[7] zlibbioc_1.2.0       
> 

--
Sent via the guest posting facility at bioconductor.org.