Hi all,

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!

Hint:

`Type`

is a linear combination of`patient`

, which is causing the error.Patientis nested withinType.I want to considerPatientas a block effect while testing for change at time T1 between C and A. Just can't reach the exact idea here!is the lowercase

`patient`

here a typo?`design <- model.matrix(~Type+patient+Type:Time`

)cause it appears uppercase in the matrix

Nope. It's all good in the case. It is actually "patient", I wrote here with upper-case! Problem is in specifying the model matrix.