I am working with edgeR to perform differential expression on rna-seq data.
I have a design with two variables : type (obese/normal) and treatment
type is a vector with two levels (obese/normal)
treatment is a vector with 5 levels ( 5 different treatments)
But when I perform this line of code : design_matrix = model.matrix(~0+type+treatment)
the design_matrix that results have only 6 columns : typeLean, typeObese and only 4 columns for treatments ( the treatment that appears to be the first level of the treatment vector is not in my design_matrix ! )
Does anyone knows why ? How could I have all the treatments in my design_matrix ?
Have a good day