Dear Bioconductor-user and developers, I have used the software RMAexpress (version 0.2) written by Ben Bolstad (http://www.stat.berkeley.edu/users/bolstad/RMAExpress/RMAExpress.html ) and normalized with it Affymetrix HG-U133A chips. In the RMAexpress -homepage is written, that I should get the same result as the ?expresso? and ?rma? from Bioconductor-affy-package version 1.2.13. Does anyone knows, if there is a difference between the ?expresso? and ?rma? from affy-package version 1.2.13 and the version 1.3.28? And if yes, what kind of difference? Will I obtain than complete different expression value? I have to analyze my normalized data (with RMAexpress) with data normalized with the affy-package version 1.3.28. And I am afraid, I am not obtaining the same expression value. Which one are the ?right? one? Thank you for any kind of help! nissa

There should be no difference in the RMA expression measures produced by expresso(), rma() or RMAExpress in current versions and in all versions of the affy package since 1.2.13. ie the claim would also hold true for 1.3.28 On Wed, 2004-10-06 at 08:04, Nissa Boucherot wrote: > Dear Bioconductor-user and developers, > > I have used the software RMAexpress (version 0.2) > written by Ben Bolstad > (http://www.stat.berkeley.edu/users/bolstad/RMAExpress/RMAExpress.ht ml) > and normalized with it Affymetrix HG-U133A chips. In > the RMAexpress -homepage is written, that I should get > the same result as the ?expresso? and ?rma? from > Bioconductor-affy-package version 1.2.13. Does anyone > knows, if there is a difference between the ?expresso? > and ?rma? from affy-package version 1.2.13 and the > version 1.3.28? And if yes, what kind of difference? > Will I obtain than complete different expression > value? > I have to analyze my normalized data (with RMAexpress) > with data normalized with the affy-package version > 1.3.28. And I am afraid, I am not obtaining the same > expression value. Which one are the ?right? one? > Thank you for any kind of help! > > nissa > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad