I'm sorry to trouble you guys. I have a doubt about my design matrix.

I have RNA-seq data for 2 different genotype of trees with
0hour(control) and after treatment 3hours,24hours,and 48hours. The
experiment design like following:

                    Treatment
  Tree H1  Ctrl  3hrs  24hrs  48hrs
  Tree H2  Ctrl  3hrs  24hrs  48hrs
  Tree L1  Ctrl  3hrs  24hrs  48hrs
  Tree L2  Ctrl  3hrs  24hrs  48hrs

I have assigned 2 factor vectors as:
  "tree" --> vector for the trees.
  "trtTime" --> vector for the control and after treatment time.

I would like to study which genes/tags that are differential expressed
in these H and L trees across the after treatment time points.

Can I assign my design matrix in this way:

  design <- model.matrix(~trtTime+tree) OR design <-model.matrix(~tree+trtTime)

I may wrong in this case as I'm not a statistician nor R programming
geek. Thus, could someone kindly please light me?

I appreciate very much for your help.

Best regards,
KJ Lim

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