Hello I have a dataset with a mixture of U95A and U95Av2 human chips-- which share the vast majority of probesets. I would like to use expresso and/or rma to analyse this all together. Is there a work round that will enable this?? Stephen ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}

Hi Stephen, please have a look at the function "combine" in the package "matchprobes" (development version). I would be interested in your experience with it, since we haven't been able to test it extensively on many different suitable datasets, for the lack of the latter. You will most likely still have "batch effects" or "lot effects", but if your experimental design is reasonably balanced across the two chip types, you may still get reasonable results. Best wishes Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber ------------------------------------- On Mon, 27 Oct 2003, Stephen Henderson wrote: > Hello > > I have a dataset with a mixture of U95A and U95Av2 human chips-- which share > the vast majority of probesets. I would like to use expresso and/or rma to > analyse this all together. Is there a work round that will enable this?? > > Stephen > > > ********************************************************************** > This email and any files transmitted with it are confidentia...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

you can find my proposed solution at http://www.stat.berkeley.edu/~bolstad/mixtureCDF/MixtureCDF.html This was done before the matchprobes package was around. As mentioned previously, expect batch effects etc. Ben On Mon, 27 Oct 2003, Stephen Henderson wrote: > Hello > > I have a dataset with a mixture of U95A and U95Av2 human chips-- which share > the vast majority of probesets. I would like to use expresso and/or rma to > analyse this all together. Is there a work round that will enable this?? > > Stephen > > > ********************************************************************** > This email and any files transmitted with it are confidentia...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >