[BioC] LIMMA contrast matrix help

[Gordon Smyth]

At 04:40 PM 4/06/2004, Maria Kamarinos wrote:
>Hello Everyone
>
>I am working through my data using the LIMMA users guide and have a question
>about forming a contrast matrix using a reference design. I have four samples
>in my experiment (A, B,C and D) which i compared to a common reference using
>dye swaps in a total of eight comparisons. I have generated the following
>design matrix:
>
>         A       B       C       D
>1       1       0       0       0
>2       -1      0       0       0
>3       0       1       0       0
>4       0       -1      0       0
>5       0       0       1       0
>6       0       0       -1      0
>7       0       0       0       1
>8       0       0       0       -1
>
>The comparisons that i am interested in are between A and B, C and D, B 
>and D.
>When designing my contrast matrix my initial thought was to put the following
>command into LIMMA:
>
> >contrast.matrix<-makeContrasts(A-B,C-D,B-D,levels=design)
>
>My question concerns how the dye swaps are handled in this situation. 
>Should i
>also include B-A, D-C and D-B in the contrast matrix to account for dye swaps
>or is this already done?

Already done. You're all set.

Gordon

>Thank-you
>
>Maria