I am creating
DeSeqDataSet and I am unsure whether I need to include the number of mice into the design formula. Basically, the samples look like this:
I have 4 different groups:
Wld. It is obvious that these should go into the design formula, but I am not sure about the mice number. Basically for each group, e.g.
GF, there are 4 experiments with
4 mice each. When I am trying to use both
Mouse columns as a design formula,
R is telling that I need to convert
I am a bit confused about two things here: first, as I told already, should I include this
Mouse column at all in the design formula of
DeSeqDataSet and second, if I do need it, how to convert it to factor? Any suggestions would be greatly appreciated.
It turned out that I was wrong in my initial assumptions:
Mouse# really was an ‘id’ which I did not include in the design formula. There were 4 groups of 16 mice in each for 4 trials.
What concerns me also is that if I specify design formula as
~ Groups + Mouse, the DeSeq() function starts comparing the
Mouse but not the
Groups which is the most interesting for me.