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  • DESeq2 help.. design

    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!

  • #2
    cross post on Bioc: https://support.bioconductor.org/p/66449/#66479

    We try to discourage cross posting as this duplicates the effort of the people answering questions, or at the least link to the cross post so other viewers can follow the thread.

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