[BioC] problems fitting model using manova

[David martin]

I'm having a problem to create a proper design:
For a set of patients i have extracted two cell types (tcells and 
Bcells). Fore each cell type i have measured the expression of a set of 
genes.

Please note this is not microarray data but flow data. I have a proper 
expr(eset) object that contains the expression data. I can't use the 
MAANOVA package as it is specific to arrays.


The pData looks like that
pData:
             Celltype  Patient  Group
pat1.cell1     Bcell         1       normal
pat1.cell2     Tcell         1       normal
pat2.cell1     Bcell         2      severe
pat2.cell2     Tcell         2      severe
pat2.cell1     Bcell         3      mild
pat2.cell2     Tcell         3      mild


My data.eset matrix looks like that

exprs(mydata.eset)
exprs:

        pat1.cell1  pat1.cell2 .....
gene1     0.18            1.2
gene2     0.56            1.5
gene3     0.20            1.3
gene4     0.56            2.2
...

I have problems to create the design. Basically i want to know what the 
are genes differentially expressed between the different severity groups 
by cell type and then combining cell types.

I have created
group=c(as.character(unique(phenotype$Group)))
patient=c(as.character(unique(phenotype$Patient)))
celltype=c(as.character(unique(phenotype$Celltype)))

#The function design.list is a custom copded encoded function to easily 
create the numeric values for the different variables

groups = factor(c(design.list(phenotype$Group,group)))
celltypes = factor(c(design.list(phenotype$Celltype,celltype)))
patients =  factor(c(design.list(phenotype$Patient,patient)))

 >celltypes
 > celltypes
   [1] 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1
......[112] 2 1 2 1 2 1 2 1 2 1 2
Levels: 1 2
 > length(celltypes)
122

 > groups
   [1] 1 1 1 1 2 2 2 2 2 2 2 2 1 1 2 2 2 2 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3
...[112] 1 1 1 1 1 1 1 1 1 1 1
Levels: 1 2 3
 > length(groups)
122

patients
   [1] 1  1  2  2  3  3  4  4  5  5  6  6  7  7  8  8  9  9  10 10 11 11 
[101] 51 51 52 52 53 53 54 54 55 55 56 56 57 57 58 58 59 59 60 60 61 61
61 Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 
... 61
 > length(patients)
122

fit<- manova( exprs(mydata.eset) ~ celltypes*groups , random=patient)
Error in model.frame.default(formula = exprs(mydata.eset) ~ celltypes *  :
   variable lengths differ (found for 'celltypes')

Again, I can't use the MANOVA package for this (flow cytometry data).

Any help to fit in the model would be very appreciated