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? Thank-you Maria -- Maria Kamarinos, PhD St Vincent's Institute of Medical Research 9 Princes St., Fitzroy, VIC, 3065 Ph: + 61 3 9288 2566 Fax: + 61 3 9416 2676 Email: mariak@medstv.unimelb.edu.au

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