Hi there! I would like to combine different Affymetrix ExpressionSets. Firstly I want to combine the esets of U133A and U133B chips from the samples. And if possible to do this I would like to combine that data set with data generated from U133Plus2 chips. Is there a way to do this? Best wishes Kristian _____ Dr Kristian Unger Bioinformaticist Chernobyl Tissue Bank Division of Surgery and Cancer Imperial College London Rm G02, Ground floor G Block Hammersmith Hospital Du Cane Road, London W12 0HS Tel +44-20-8383-2443 Mob +44-795-1080619 Skype kristianunger http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/ http://www.chernobyltissuebank.com [[alternative HTML version deleted]]

Dear Kristian I am afraid you will need to tell us more precisely what you mean by "combine", i.e. what is the goal or question behind it. On a trivial level, of course you can combine the datasets, using "cbind", "merge" etc. However, there are many subtleties regarding normalisation (which first you should do separately for each array type), and batch effects. The appropriate solution, if any, will depend a lot on the nature and quality of your data, and your question. Best wishes Wolfgang Unger, Kristian scripsit 01/21/2010 10:57 AM: > Hi there! > > I would like to combine different Affymetrix ExpressionSets. > > Firstly I want to combine the esets of U133A and U133B chips from the samples. And if possible to do this I would like to combine that data set with data generated from U133Plus2 chips. > > Is there a way to do this? > > Best wishes > > Kristian > > _____ > > Dr Kristian Unger > > Bioinformaticist Chernobyl Tissue Bank > > Division of Surgery and Cancer > > Imperial College London > > Rm G02, Ground floor G Block > Hammersmith Hospital > Du Cane Road, > London W12 0HS > > Tel +44-20-8383-2443 > > Mob +44-795-1080619 > > Skype kristianunger > > http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/ > http://www.chernobyltissuebank.com > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 EMBL http://www.embl.de/research/units/genome_biology/huber/contact