[BioC] Limma : Problem with lmFit() and block

[Laetitia Marisa]

Hello,

When I use the block variable in the lmFit, data in the MArrayLM have 
different dimension :

 > dim(analysis$fit)
[1] 6936    3

 > dim(analysis$fit$coef)
[1] 6936    3

 > dim(analysis$fit$genes)
[1] 2312    6


Here is the command line I've  passed and a description of the data I've 
used :

analysis$fit <- lmFit( msData, design=analysis$effects$Designmatrix , 
block = msData$block , ndups=msData$printer$ndups, 
spacing=msData$printer$spacing,  weights=NULL )

 > dim(msData)
[1] 6936   15
 > msData$block
 [1] 1 1 2 3 3 4 4 5 5 6 6 7 7 8 8
 > msData$printer$ndups
[1] 3
 > msData$printer$spacing
[1] 1

 > analysis$effects$Designmatrix
         A  B  C
Array1   1  0  0
Array2  -1  0  0
Array3   1  0  0
Array4   1  0  0
Array5  -1  0  0
Array6   0  1  0
Array7   0 -1  0
Array8   0  1  0
Array9   0 -1  0
Array10  0  0  1
Array11  0  0 -1
Array12  0  0  1
Array13  0  0 -1
Array14  0  0  1
Array15  0  0 -1

Am I doing something wrong or it is a problem in the lmFit function?

Thanks a lot.

Laetitia Marisa.