Yes, it is performed on the M-values. You have dual-channel with a 
common reference, so the stats should be done on the M-values. 
However, the design matrix will be exactly the same for a 
dual-channel experiment with common reference all in Cy3 and an 
Affymetrix data set.

Jenny

At 09:39 AM 1/26/2011, Sharon wrote:
>Hi Jenny,
>
>Thanks a lot. Does this mean the paired t-test is performed on 
>M-values but not on the intensity values (as in Affymetrix)?
>
>Thanks again,
>Sharon
>
>On Wed, Jan 26, 2011 at 2:45 PM, Jenny Drnevich 
><<mailto:drnevich@illinois.edu>drnevich@illinois.edu> wrote:
>Hi Sharon,
>
>Your experimental design is almost exactly like the Paired Samples 
>example in the limmaUsersGuide() , section 8.3. The only difference 
>is that you have dual-channel arrays. However, since all your common 
>reference are in the Cy3 channel, all the M-value ratios are already 
>in the direction you want them. You can use the Paired Samples code 
>exactly as if you had single-channel data.
>
>HTH,
>Jenny
>
>
>At 07:18 AM 1/26/2011, Sharon wrote:
>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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>
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