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David
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860
@david-3335
Last seen 6.9 years ago
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
