[BioC] Paired Data in maSigPro

[Mike Walter]

Dear List,

I have a tiem series experiment, I want to analyse with maSigPro. The data are from blood samples from 8 donors taken at 4 different timepoints under 2 treatments. My design matrix would look like this:

> dm
 Time Replicate Control LPS
I10R029a01.CEL    0         1       1   0
I10R029a03.CEL    0         1       1   0
I10R029a04.CEL    0         1       1   0
I10R029a05.CEL    0         1       1   0
I10R029b01.CEL    0         2       0   1
I10R029b03.CEL    0         2       0   1
I10R029b04.CEL    0         2       0   1
I10R029b05.CEL    0         2       0   1
I10R029c01.CEL    0         1       1   0
I10R029c03.CEL    0         1       1   0
I10R029c04.CEL    0         1       1   0
I10R029c05.CEL    0         1       1   0
I10R029d01.CEL    0         2       0   1
I10R029d05.CEL    0         2       0   1
I10R029d06.CEL    0         2       0   1
I10R029d07.CEL    0         2       0   1
I10R029e05.CEL    1         3       1   0
I10R029e06.CEL    1         3       1   0
I10R029e07.CEL    1         3       1   0
I10R029e08.CEL    1         3       1   0
I10R029f01.CEL    1         4       0   1
I10R029f05.CEL    1         4       0   1
I10R029f06.CEL    1         4       0   1
I10R029f07.CEL    1         4       0   1
I10R029g01.CEL    1         3       1   0
I10R029g02.CEL    1         3       1   0
I10R029g03.CEL    1         3       1   0
I10R029g04.CEL    1         3       1   0
I10R029h01.CEL    1         4       0   1
I10R029h02.CEL    1         4       0   1
I10R029h03.CEL    1         4       0   1
I10R029h04.CEL    1         4       0   1
I10R029i01.CEL    2         5       1   0
I10R029i02.CEL    2         5       1   0
I10R029i03.CEL    2         5       1   0
I10R029i04.CEL    2         5       1   0
I10R029j01.CEL    2         6       0   1
I10R029j02.CEL    2         6       0   1
I10R029j03.CEL    2         6       0   1
I10R029j04.CEL    2         6       0   1
I10R029k01.CEL    2         5       1   0
I10R029k02.CEL    2         5       1   0
I10R029k03.CEL    2         5       1   0
I10R029k04.CEL    2         5       1   0
I10R029l01.CEL    2         6       0   1
I10R029l02.CEL    2         6       0   1
I10R029l03.CEL    2         6       0   1
I10R029l04.CEL    2         6       0   1
I10R029m01.CEL    3         7       1   0
I10R029m02.CEL    3         7       1   0
I10R029m03.CEL    3         7       1   0
I10R029m04.CEL    3         7       1   0
I10R029n01.CEL    3         8       0   1
I10R029n02.CEL    3         8       0   1
I10R029n03.CEL    3         8       0   1
I10R029n04.CEL    3         8       0   1
I10R029o01.CEL    3         7       1   0
I10R029o02.CEL    3         7       1   0
I10R029o03.CEL    3         7       1   0
I10R029o04.CEL    3         7       1   0
I10R029p01.CEL    3         8       0   1
I10R029p02.CEL    3         8       0   1
I10R029p03.CEL    3         8       0   1
I10R029p04.CEL    3         8       0   1

However, since the samples were drawn from the same donors, I'd like to ask if there is a way to include this information also in the design matrix like in a paired analysis as in limma?

Thanks for your input and kind regards,

Michael