[BioC] Limma; a kind of extended paired analyses with or without treatment

[john herbert]

Dear all.
I have been pondering about constructing a design matrix based on the
Limma user guide, where I combine a time course with a paired
analyses. The targets file looks like;

Sample	treatment	time
1	control	24
1	control	72
1	control	0
1	treatment	24
1	treatment	72
2	control	24
2	control	72
2	control	0
2	treatment	24
2	treatment	72
3	control	24
3	control	72
3	control	0
3	treatment	24
3	treatment	72

Sample number refers to an individuals cancer cells, treatment refers
to added drug or not and numbers are in hours (time elapsed). So it is
a kind of paired, as patient variability is to be considered. The
control sample at 0 is the same as treatment at time 0 as these are
the same cells without any time/treatment.

Please could someone help me understand how I can construct a design
matrix and to understand how I can extract differently expressed genes
that come about due to time, due to treatment and interaction of them
both.

Any pointers appreciated, though I am trying to see if the examples in
the manual can be applied to this scenario.

Thank you.

John.