Dear Xiaokuan slight differences can be expected due to the probe sampling that is used in the vsn2 method for AffyBatch to increase the speed of the computation. You can switch off the sampling e.g. by specifying "subsample=0" in the call to vsnrma. And you can make the sampling deterministic by calling set.seed before vsnrma. However, such differences should always be small compared to the precision of the data themselves - i.e., they should be negligible. If they are not, something is foul. I would be interested in a reproducible example: sessionInfo(), exact script used, the necessary data objects. Best wishes Wolfgang On Jun/30/10 9:26 PM, Xiaokuan Wei wrote: > Dear List, > > I have applied "vsnrma" commpand to an affybatch object. But for the same object, if I run multiple times vsnrma, it gives me different values. > i.e. > > dat1<-vsnrma(obj) > dat2<-vsnrma(obj) > dat3<-vsnrma(obj) > > > dat1,dat2,and dat3 are different. It's not just numerically marginally different, but rather larget different. > for example, probe A, for dat1, the value is 3, dat2 is 4, dat3 is 5. > > Could Wolfgang or someone explain this to me? Is there a way to seed a value and make the results same? > > Thank you. > > Xiaokuan > > > > [[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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber