Hi list, I cant reproduce results that I got before. I am fairly sure that it is to do with incompatible versions I am using R 1.8.1 affy 1.3.26 affyPLM 1.0.0 AffyExtensions 0.6-2 which from the history line on Ben Bolstad's page should be OK. Does anyone have any ideas? Also -- This is not the first time I have had a problem in producing a paper trail for an analysis and then reproducing it. How do other people handle this problem? rlm.output <- threestep(Dilution,background.method="RMA.2", + normalize="quantile",summary.method="rlm") Background correcting Normalizing Calculating Expression Error in hasTsp(x) : cannot assign `tsp' to zero-length vector >