Hi All please ignore, we have relised the design matrix needs reworking to give meaningful results for the limited slides we have in this particular experiment ;-) Jason > running duplicateCorrelation in limma > > cor <- duplicateCorrelation(nwaMA, ndups=2, spacing=840, design) > > I have three arrays with the following design > a b c > Array 1 1 0 0 > Array 2 0 -1 0 > Array 3 0 0 -1 > > The layout is: > $ngrid.r > [1] 12 > $ngrid.c > [1] 4 > $nspot.r > [1] 21 > $nspot.c > [1] 20 > > the correlation returned is 1 for every gene on the array ? -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919