[BioC] Design matrix for simple time course

[michael watson (IAH-C)]

Hi 

I am trying to create a design matrix for a simple, one-channel
time-course experiment.

I have five time points with three replicated arrays at each time point.
I want to set up the design matrix.

I tried using:

	model.matrix(~factor(rep(1:5,each=3)))

Vaguely following the tutorial here
(http://bioinf.wehi.edu.au/marray/jsm2005/lab5/lab5.html)

However, I only have one factor to model, time.

The matrix that comes out as the first column all of ones, the
intercept.  What I (think) I want is the first column to have three 1's
and the rest 0's.

I guess I'm really struggling as I don't know what the difference is
between the output of model.matrix, with an Intercept column of all 1's,
and the design matrix I want, which has a first column of three 1's at
the top and the rest 0's.

:-s

Thanks
Mick