[BioC] problems fitting model using manova
Martin Morgan
mtmorgan at fhcrc.org
Thu Dec 10 14:19:42 CET 2009
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
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