edgeR, how to write the model matrix for comparison?

Question

[TM]

Hi, I am quite new to edgeR. I would like to ask how to write the model matrix for comparison. I have 9 samples from 3 donors. Each donor has 3 samples, representing 3 structures. For example Donor 1 has structure A,B,C Donor 2 has structure A,B,C Donor 3 has structure A,B,C

I would like to see the differentially expressed gene of structure B (taking structure A &C as reference) Is it possible to analyze structure A vs B, B vs C & A vs C in each donor and combine together? or Do I need to group same structure from each donor as one group and finally I got 3 groups to compare?

Can you give me suggestion and also how to write the model matrix for comparison?

Thank you in advance!

[brunobsouzaa]

Yes, It's possible. Take a look into the documentation, It's pretty much straightforward!

[TM]

Thank you!!