Tom wrote: > Some additional information: > > My data comes from two different type of microarray: hgu133a and hthgu133a > I want pre-process my data to obtain only one ExpressionSet that contain the > merged data. > > What I want to do is: > - merge the two batches with combineAffyBatch function > - normalize the data (for example with rma) > > Is this a good way to pre-process my data? > > Any suggest is appreciated. > Thanks in advance. > > _______________________________________________ > 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 > > My advice is that you will want to be very careful here because there are strong batch effects for the different chip types. That is, a given probeset "X" will behave very differently on one chip type than on another. I would try to avoid doing this if possible, but if you cannot, then you will probably have to find a statistician to help you try to adjust between these two different groups. Hopefully you will have all the things you want to compare represented well on both platforms? Otherwise your going to find yourself hip-deep in false positives. Marc