Hi I'm having difficulty with a design matrix in the duplicateCorrelation function in limma I have 15 slides and M values for each of them: [,1] to [,15] however when I specify the following matrix W2minusW0 M2minusM0 M2minusW2 M0minusW0 M22minusM20 M22minusW2 M20minusW0 1 0 0 0 0 0 0 -1 2 0 0 0 0 0 0 1 3 0 0 0 0 0 1 0 4 0 0 0 0 0 -1 0 5 0 0 -1 0 0 0 0 6 0 0 1 0 0 0 0 7 0 0 0 0 1 0 0 8 0 0 0 0 -1 0 0 9 0 0 0 -1 0 0 0 10 0 0 0 1 0 0 0 11 1 0 0 0 0 0 0 12 -1 0 0 0 0 0 0 13 0 1 0 0 0 0 0 14 0 -1 0 0 0 0 0 15 -1 0 0 1 0 0 0 cor <- duplicateCorrelation(object$M, design="designmatrix",spacing=648) Error in duplicateCorrelation(object$M, design = "designmatrix", : Number of rows of design matrix does not match number of arrays I only appear to have had this problem since I changed limma versions ??? using R 1.9.0 limma 1.6.7 Does anyone know of a easy way either contruct the above matrix OR check wether the matrix is suitable for dupcor.... I've tried both matrix and dataframes both with the same error any help greatly recieved Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

At 10:25 PM 13/06/2004, Jason Skelton wrote: >Hi > >I'm having difficulty with a design matrix in the duplicateCorrelation >function in limma >I have 15 slides and M values for each of them: [,1] to [,15] >however when I specify the following matrix > > W2minusW0 M2minusM0 M2minusW2 M0minusW0 M22minusM20 M22minusW2 M20minusW0 >1 0 0 0 0 0 0 -1 >2 0 0 0 0 0 0 1 >3 0 0 0 0 0 1 0 >4 0 0 0 0 0 -1 0 >5 0 0 -1 0 0 0 0 >6 0 0 1 0 0 0 0 >7 0 0 0 0 1 0 0 >8 0 0 0 0 -1 0 0 >9 0 0 0 -1 0 0 0 >10 0 0 0 1 0 0 0 >11 1 0 0 0 0 0 0 >12 -1 0 0 0 0 0 0 >13 0 1 0 0 0 0 0 >14 0 -1 0 0 0 0 0 >15 -1 0 0 1 0 0 0 > >cor <- duplicateCorrelation(object$M, design="designmatrix",spacing=648) The design matrix must be a _matrix_. You've input a character string. This would not work in any version of limma. If "designmatrix" is the name of your matrix, perhaps you simply need to remove the double-quotes. Gordon >Error in duplicateCorrelation(object$M, design = "designmatrix", : > Number of rows of design matrix does not match number of arrays > >I only appear to have had this problem since I changed limma versions ??? > >using R 1.9.0 >limma 1.6.7 > >Does anyone know of a easy way either contruct the above matrix >OR >check wether the matrix is suitable for dupcor.... > >I've tried both matrix and dataframes both with the same error > >any help greatly recieved >Jason