[BioC] problems fitting model using manova

[Martin Morgan]

Hi David --

David martin wrote:
> 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')

manova fits the model to *columns* so expects t(exprs(mydata.eset)). Martin

> 
> Again, I can't use the MANOVA package for this (flow cytometry data).
> 
> Any help to fit in the model would be very appreciated
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793