Hi,

We have the following design for our twin-sample array analysis:

File       Cy3 Cy5    Twin
403797 Ref   A       1
343724 Ref   A       2
343857 Ref   A       3
403784 Ref Con     1
343720 Ref Con      2
343960 Ref Con      3

We would like to compare A-Con, so, I have constructed the following design
matrix:

Intercept T2    T3   A Con
1             0       0     1   0
1             1       0     1   0
1             0       1     1   0
1             0       0     0   1
1             1       0     0   1
1             0       1     0   1

and then constructed the contrast matrix for comparing A-Con:

                Contrasts
Levels      AvsCon
  Intercept    0
  T2           0
  T3           0
  A                1
  Con           -1

Could you please tell us whether the design and contrast matrices are
appropriate for comparing A-Con?

Thanks in advance.

Kind regards,
Sharon

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