Hello, I need an explanation of how the design matrix influences the consensus correlation of the duplicateCorrelation function when accounting for technical replicates. Here is my specific example: Design matrix: > design RJf RJm WLf WLm 1 0 0 0 1 2 0 0 0 1 3 0 0 0 1 4 0 0 0 1 5 0 0 0 1 6 0 0 0 1 7 0 0 0 1 8 0 0 0 1 9 0 0 1 0 10 0 0 1 0 11 0 0 1 0 12 0 0 1 0 13 0 0 1 0 14 0 0 1 0 15 0 0 1 0 16 0 0 1 0 17 0 1 0 0 18 0 1 0 0 19 0 1 0 0 20 0 1 0 0 21 0 1 0 0 22 0 1 0 0 23 0 1 0 0 24 0 1 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 # each second slide is a replicate of the first (eg. 1 and 2 are replicates, then 3 and 4,... etc.). There are also 4 groups that I want to compare, with 4 individuals in each group (each duplicated). So I continue with the duplicateCorrelation: # > cor <- duplicateCorrelation(Mmatrix_ny, design=design, + block=c(1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13,14 ,14,15,15,16,16)) > cor$cor [1] -0.03060575 # which is a pretty bad correlation so I probably should just use the technical replicates as biological replicates (the limma user guide says). But in another comparison I want to put all the arrays in 2 groups, see design matrix: > designWLRJ RJ WL 1 0 1 2 0 1 3 0 1 4 0 1 5 0 1 6 0 1 7 0 1 8 0 1 9 0 1 10 0 1 11 0 1 12 0 1 13 0 1 14 0 1 15 0 1 16 0 1 17 1 0 18 1 0 19 1 0 20 1 0 21 1 0 22 1 0 23 1 0 24 1 0 25 1 0 26 1 0 27 1 0 28 1 0 29 1 0 30 1 0 31 1 0 32 1 0 # and then do the duplicateCorrelation function and get a different correlation. # > corWLRJ <- duplicateCorrelation (Mmatrix_ny, design=designWLRJ, + block=c(1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13,14 ,14,15,15,16,16)) > corWLRJ$cor [1] 0.01745252 # Moreover when I compute the consensus correlation without using a design matrix I get 0.1073055. I know from looking through previous posts and a lot of help from Johan L. that the way the blocking is set up and using the design matrix in these situations is correct. So how is the consensus correlation actually being calculated in the above situations? (in loose mathamatical terms if possible, as you can probably tell from my question). Thanks a lot for your time, Carolyn -- Carolyn Fitzsimmons Dept. Medical Biochemistry and Microbiology Uppsala University Box 597/BMC SE-751 24 SWEDEN E-mail: Carolyn.Fitzsimmons at imbim.uu.se Tel: +46 (0)18 471 4593 Mobile: +46 (0)73 704 1248