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Old 01-04-2016, 02:21 AM   #1
ea11
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Location: Southampton

Join Date: Jun 2015
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Default 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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