Hi,

I am finding it difficult to come up with an appropriate design matrix for
my 2-color microarray dataset.  This dataset has dye-swap, pooled RNA,
replicates and more than 2 conditions. The following is the scheme of my
data.

We have 3 groups (CTRL, T1, T2) and the RNA was extracted from 4 animals for
each group. For CTRL group, RNA from animals 1 & 2 (ctrl 1/2) were pooled
together, it is the same for animals 3&4 (ctrl 3/4).

CTRL Cy3 vs T1 Cy5:                  T1 Cy3 vs CTRL Cy5:
ctrl 1/2 vs T11                      T11 vs ctrl 3/4
ctrl 1/2 vs T12                      T12 vs ctrl 3/4
ctrl 1/2 vs T13                      T13 vs ctrl 3/4
ctrl 1/2 vs T13                      T14 vs ctrl 3/4


T2 Cy3 vs CTRL Cy5:                   CTRL Cy3 vs T2 Cy5:
T21 vs ctrl 1/2                       ctrl 3/4 vs T21
T22 vs ctrl 1/2                       ctrl 3/4 vs T22
T23 vs ctrl 1/2                       ctrl 3/4 vs T23
T24 vs ctrl 1/2                       ctrl 3/4 vs T24


T1 Cy3 vs T2 Cy5:                     T2 Cy3 vs T1 Cy5:
T11 vs T21                            T21 vs T11
T12 vs T22                            T22 vs T12
T13 vs T23                            T23 vs T13
T14 vs T24                            T24 vs T14


In addition, we have 4 spot replicates for each probe.  I would like to
compare  CTRL vs T1, CTRL vs T2 and T1 vs T3.  Can anyone please suggest me
an appropriate design matrix for this experiment?

Thanks in advance.

Best regards,
Sharon

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