How can I create a Design (model)Matrix for edgeR package usage?

Question

[rekren]

It can be silly question but, I didn't use edgeR package for my analysis before.

I have 12 samples of miRNA reads in my data.frame which belong the "before_treatment" and "after_treatment" cases of 6 patients.

Clinical outcomes are known for these 6 patients. 3 groups of outcomes were observed on these patients. These groups are; "positive_response", "negative_response" and "no_clear_response."

I am aiming to uncover the most upregulated/downregulated miRNAs for each response groups on the given patients' data.

How can I form proper design matrice with the model.matrix command of R ?

Answer 1

[h.mon]

See section 3.5 of the edgeR Users Guide, pages 37-39. It describes the same design you want to implement.