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  • Design matrix for edgeR help

    Hi,

    I am attempting to create a design matrix in edgeR to determine differentially expressed genes, but I am unsure on the notation to use as I am relatively new to R and not a statistician in any way.

    Basically, the experimental design is as follows:

    We have two treatments (A and B), each treatment had two cages and in each cage, there were 3 mice. Therefore in total, we have 6 mice for each treatment, coming from 2 cages for each treatment (total of 4 cages). We are not interested in the effect of the different cages, but are interested in differentially expressed genes between the 2 treatments (A and B).

    So what I was wondering is what the design matrix would be taking into account that cage is nested in treatment. Would it be one of the following or something completely different:

    PHP Code:
    design <- model.matrix(~cage/treatment)

    design <- model.matrix(~treatment*cage)

    design <- model.matrix(~cage %intreatment
    Thanks for any help

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