Dear edgeR community,

Good day.

I have sets of RNA-Seq data of 2 phenotype (HighS, LowS) plants with area
TZ & SW (control).  I used exactTest to study which genes that are
differential expressed in area TZ compare to SW of each phenotype.

I would like to know do the phenotypes have effect on the area, in this
case I should use glmLRT test. Before fit into the GLM, I defined my design
matrix as:

  ~phenotype+area

Could someone please advice me regarding the design matrix? Should I define
my design matrix as  ~area+phenotype ?

Thank you very much for your time and help.

Have a nice weekend.

Best regards,
KJ Lim

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