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Hi Han, It depends on what level of sharing you want. You can do it at the level of UniGene/GenBank, 25mer, EntrezGene (and probably a few others). That is probably the most important decision. One way to do this is to first decide what you want to match on and then map all the probes on the chip to the identifier you are going to use (the annotation packages can be used for this and I suspect that biomaRt could do it as well)- and then use something like intersect to find the common ones. Best wishes Robert weinong han wrote: > Hi ,all > > I want to list the shared/common genes from between different genechips, such as Affymetrix HG_U95A, Affymetrix HG_U95Av2, Affymetrix HG_U133A and some in-house genechips with R2.1.0 patched under Windows XP. > > However, I didn't know what method/package is fit for the analysis. Anyone have the experience on it? Any suggestions and advice will be much appreciated. > > Many thanks in advance. > > > > Best Regards > > Han Weinong > hanweinong at yahoo.com > > __________________________________________________ > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >