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.