Dear Alex, Do you have the same number of replicate spots for every gene of interest and are the replicate probes identical? If so, see the case study in limma User's Guide on "Within array replicate spots". If only some of your genes are replicated, or if the probes are not identical, I would strongly advice you not to attempt to pre-emptively average the spots. There is little to be gained and much to be lost. I don't understand you comment about ignoring spots with zero weight. limma already does this. Best wishes Gordon >[BioC] averaging replicates within arrays >alex lam (RI) alex.lam at bbsrc.ac.uk >Tue Nov 8 23:49:46 CET 2005 > >Dear Colleagues, > >Hi, I am a first year PhD student recently started on a project involving >microarray data analysis at the Roslin Institute in Scotland. I have >managed to follow the limma vignette in loading the data and performed >the default normalization within arrays. On each array, probes of the same >genes have been placed in more than one spot. What I would like is to do >is to group spots by gene names in MA$genes and calculate the average >logratio as the expression level (better still, ignore the spots with zero >weight). > >I guess I can dump the data and process it in perl but would like to know >how to do this a bit more elegantly in R. Your help is greatly appreciated. > >Many thanks, >Alex