Hi All,

My experiment has 3 factors: tissue (2 tissues), time points (3 time points)
and  treatment (untreated vs treated).
I have 24 affy chips for each tissue. Within this, I have 8 chips for each
time point with 4 for untreated, 4 for treated.
I would like to see the treatment effect across time points and tissues. I
am trying to construct the design matrix
following Affy 2x2 factorial experiment described in the Limma's user guide
with less success.  Any suggestions for
building the design matrix?

Thanks in advance.

Regards,
Sharon

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