Entering edit mode
3.4 years ago
chatterjee.arumoy
▴
50
Hi, I am using maSigPro to do a single series time course RNA-seq analysis. My design matrix looks like as follow:
> design
Time Replicates Group Batch
Array1 0 1 1 A
Array2 0 2 1 A
Array3 0 3 1 B
Array4 30 1 1 A
Array5 30 2 1 A
Array6 30 3 1 B
Array7 60 1 1 A
Array8 60 2 1 A
Array9 60 3 1 B
Array10 120 1 1 A
Array11 120 2 1 A
Array12 120 3 1 B
I would like to know how to include the aforementioned batch effects in the maSigPro? Is there a way to do it similar to
design = model.matrix(~ 0 + conditions + batch, data=y$samples)
as in edgeR?
Kindly help. Thanks a lot. Arumoy.