DESeq2 help.. design

[pinuscatcus]

hello all,

So in my experiment, we have 2 different treatments applied to 2 groups of mice (ctrl vs trt, 5 each). Within each mouse, we took 2 different tissue types (tissue, A and B). We'd like to know basically how trt different (within each tissue type and overall) (I guess after the model design, we will do contrast of various sort?). Since each experimental unit (mice) have 2 tissue types, it would be wise to block on individuals. In essence, we have:
sampleCondition <- c(
rep("T",2),
rep("C",4),
rep("T",8),
rep("C",6)
)

individual <- c(
rep("11",2),
rep("12",2),
rep("13",2),
rep("14",2),
rep("15",2),
rep("16",2),
rep("17",2),
rep("18",2),
rep("19",2),
rep("20",2)
)

tissue=rep( c("A","B"), 10)

sampleTable<-data.frame(sampleName=sampleFiles,
filename=sampleFiles,
treatment=sampleCondition,
tissue=tissue,
individual=individual)

dds<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable,
directory=directory,
design=~ individual + individual:tissue + individual:treatment
)

and also tired:
design=~ individual + tissue + tissue:treatment

both of these design gave us:
Error in DESeqDataSet(se, design = design, ignoreRank) :
the model matrix is not full rank, so the model cannot be fit as specified.
one or more variables or interaction terms in the design formula
are linear combinations of the others and must be removed

I am stuck here,... sort thinking my model might be wrong? Thanks for any help!

[Michael Love]

cross post on Bioc: https://support.bioconductor.org/p/66449/#66479

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