[BioC] DESeq2 multifactorial formula

[Ugo Borello]

Good morning,

I am trying to run DESeq2 with this design formula
design <- (~batch+sex+tissue)

This is what I do from a count matrix:
>library(DESeq2)

>countTable<- read.table('matrix.txt', header=TRUE, row.names=1)


>ConDesign<- data.frame(row.names = colnames(countTable),
                       batch = factor(c("1", "2", "3", "1", "2", "3")),
                       sex = factor(c("F", "F", "M", "F", "F", "M")),
                       tissue = factor(c("Cx", "Cx", "Cx",
                                  "BrS", "BrS", "BrS")))

>ConDesign
               batch sex  tissue
Cx_1        1       F     Cx
Cx_2        2       F     Cx
Cx_3        3       M    Cx
BrS_1       1       F    BrS
BrS_2       2       F    BrS
BrS_3       3       M   BrS


When I run 
>xx<- model.matrix(~batch+sex+tissue, ConDesign)

I get
>xx
                (Intercept) batch2 batch3 sexM tissueBrS
Cx_1                       1      0      0          0          0
Cx_2                       1      1      0          0          0
Cx_3                       1      0      1          1          0
BrS_1                      1      0      0          0          1
BrS_2                      1      1      0          0          1
BrS_3                      1      0      1          1          1

But when I run:
>dse<- DESeqDataSetFromMatrix(countData= countTable,
                             colData = ConDesign,
                             design =  (~batch+sex+tissue))



I get this error message:
Error in validObject(.Object) :
  invalid class ³DESeqDataSet² object: the model matrix is not full rank,
i.e. one or more variables in the design formula are linear combinations of
the others

Where is my mistake?

Thank you for your help,
Ugo


> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
base     

other attached packages:
 [1] org.Hs.eg.db_2.9.0      RSQLite_0.11.4          DBI_0.2-7
AnnotationDbi_1.22.6
 [5] DESeq2_1.0.19           RcppArmadillo_0.3.910.0 Rcpp_0.10.4
lattice_0.20-23    
 [9] Biobase_2.20.1          GenomicRanges_1.12.5    IRanges_1.18.3
BiocGenerics_0.6.0 

loaded via a namespace (and not attached):
 [1] annotate_1.38.0    genefilter_1.42.0  grid_3.0.1         locfit_1.5-9.1
RColorBrewer_1.0-5
 [6] splines_3.0.1      stats4_3.0.1       survival_2.37-4    tools_3.0.1
XML_3.95-0.2      
[11] xtable_1.7-1