Dear Gordon, I am analysing a simple two-colour microarray experiment camparing strain A vs. strain B with 3 biological and two technical replicates (dye swap). Hence, my experiment is similar to your example in section 11.1 of the limma user's guide. Our array has four within-array replicate spots for each gene. As the "block" argument in the limma function "lmFit" must be NULL if ndups is larger than 2 I wonder how I can handle both technical and within-array replicates? In advance, many thanks for any suggestions! Pie _______________________________________________________ Dr Pie Mueller Vector Research Division Liverpool School of Tropical Medicine Pembroke Place Liverpool L3 5QA UK Tel. +44 (0)151 705 3123 (office) Tel. +44 (0)151 705 3140 (Gwen Finnegan Dept Secretary) Fax. +44 (0)151 705 3369

Sorry, didn't see that this question has been addressed earlier... Still what would you suggest? Compute the mean values from the replicate spots on each array after normalisation and use those for fitting the linear model, or neglecting the "block" effect of the dye-swap? A similar problem occurs if one considers separate channel analysis of two-colour data. What is the best way to create a new MAlist object with means from my original object containing the values for each replicate spot? To use the function "aggregate"? Couldn't figure out with my basic R knowledge... Thanks, Pie Dear Gordon, I am analysing a simple two-colour microarray experiment camparing strain A vs. strain B with 3 biological and two technical replicates (dye swap). Hence, my experiment is similar to your example in section 11.1 of the limma user's guide. Our array has four within-array replicate spots for each gene. As the "block" argument in the limma function "lmFit" must be NULL if ndups is larger than 2 I wonder how I can handle both technical and within-array replicates? In advance, many thanks for any suggestions! Pie _______________________________________________________ Dr Pie Mueller Vector Research Division Liverpool School of Tropical Medicine Pembroke Place Liverpool L3 5QA UK Tel. +44 (0)151 705 3123 (office) Tel. +44 (0)151 705 3140 (Gwen Finnegan Dept Secretary) Fax. +44 (0)151 705 3369