[BioC] Using Limma for common reference and paired samples

[Jenny Drnevich]

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
>
>         [[alternative HTML version deleted]]
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at r-project.org
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
>http://news.gmane.org/gmane.science.biology.informatics.conductor