**10**wrote:

Good morning,

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 ?

Thank you,

Have a good day

**7.4k**• written 18 months ago by Aurora •

**10**