I have paired sample data set and I'm not too sure how to set up the design matrix in edgeR for differential expression.
I have paired samples from women who have cancer (cancer tissue and benign tissue were obtained), these women were also divided into overweight and not overweight (by BMI >30). I have 6 patient samples for overweight and another 6 for not overweight all of which are paired
The samples are as below:
Patient BMI>30 Cancer tissue
1 No Yes
1 No No
2 No Yes
2 No No
3 Yes Yes
3 Yes No
4 Yes Yes
4 Yes No
In the edgeR manual under '3.5 Comparisons both between and within subjects' there is a multilevel design and I think that is the most appropriate. Or that I compare the BMI>30 patients. Then compare the BMI<30 patients.
Is this the same? EdgeR - comparison between subjects is not working
It looks like we're in the same group