I am working on a RNA-Seq data where my factor set looks like the following:
Type Patient Time C 3 T0 C 3 T1 C 8 T0 C 8 T1 C 9 T0 C 9 T1 C 10 T0 C 10 T1 C 5 T1 C 11 T1 A 1 T0 A 1 T1 A 4 T0 A 4 T1 A 6 T0 A 6 T1 A 7 T0 A 2 T1
Here, I want to see the change in expression at time T1 between C and A.
I tried to specify the model matrix in edgeR as:
design <- model.matrix(~Type+patient+Type:Time)
But, when I tried to use "
estimateGLMCommonDisp" command, it shows an error saying that the design is not of full rank.
Could anyone please help me by correcting my model matrix?
Thanks in advance!