Dear Karin, the software is open source, so you can always find out what it does. In your case, type require("affy") getMethod(hist, "AffyBatch") this will point you to a function "plotDensity.AffyBatch", and when you type this function name, plotDensity.AffyBatch you will get its definition. This will show that after some preprocessing, it calls plotDensity Now you are ready to take these functions and adapt them to your needs. Using this kind of protocol, you can always figure out what is going on. Best wishes Wolfgang Sean Davis ha scritto: > On Thursday 12 April 2007 09:16, Karin Lagesen wrote: >> I am testing different normalization methods for some affy chips. I am >> looking for a way to get the same plot for the resulting exprset that >> I end up with after running vsn on an abatch object that I would get >> from running hist(abatch). >> >> I know that I can probably use densityplot from the lattice package, >> but then they start talking about kernel functions and smoothing, and >> I don't know enough about that to know what I should choose for >> densityplot to get the "same" as is in the hist function for an >> AffyBatch object. > > Hi, Karin. > > Does this do what you want? > > plotDensity(exprs(myExprSet)) > > where myExprSet is your expression set. > > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber