Hi, everybody, I have analyzed a set of CEL files with rma() and with expresso(), using the following options: normalize.method=qspline, bg.method=rma, pmcorrect.method=pmonly, summary.method=medianpolish. As probably some people are aware, the expression intensity values obtained from both methods are not identical. What is the reason? Maybe RMA() uses rma2 as the method to correct for background values? If so, what is the difference between these two methods of background correction? TIA Christian [[alternate HTML version deleted]]

As of version 1.2.13 of the affy package, by default you should get the same expression values from both rma() and expresso(). One other point I note is that you used normalize.method="qspline" in your expresso() call. rma() does the equivalent of normalize.method="quantiles". Thanks, Ben On Fri, 2 May 2003, [iso-8859-1] cmprobst wrote: > Hi, everybody, > > > I have analyzed a set of CEL files with rma() and with expresso(), using the following options: normalize.method=qspline, bg.method=rma, pmcorrect.method=pmonly, summary.method=medianpolish. > > As probably some people are aware, the expression intensity values obtained from both methods are not identical. > > What is the reason? Maybe RMA() uses rma2 as the method to correct for background values? If so, what is the difference between these two methods of background correction? > > TIA > > Christian > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

I think you would have to use normalize.method=quantiles to get rma. Also, using bg.correct=rma2 gives results similar to what you would get with Bioconductor 1.1. If you want results similar to rma in 1.2, you have to use bg.correct=rma. You can see the details of what bg.correct=rma does by looking at the functions bg.adjust and bg.parameters. Bg.correct=rma is compiled code, so it is more difficult to inspect. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "cmprobst" <cmprobst@terra.com.br> 05/02/03 12:46PM >>> Hi, everybody, I have analyzed a set of CEL files with rma() and with expresso(), using the following options: normalize.method=qspline, bg.method=rma, pmcorrect.method=pmonly, summary.method=medianpolish. As probably some people are aware, the expression intensity values obtained from both methods are not identical. What is the reason? Maybe RMA() uses rma2 as the method to correct for background values? If so, what is the difference between these two methods of background correction? TIA Christian [[alternate HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor