Dear all, I have a question considering the bug in the RMA function eset <- rma() that was highlighted (by Hu Wei) in the end of January this year. He found that the results from this rma streamline version differed from the results obtained using the individual commands: eset<. expresso(), normalize.method=quantiles, bg.method="rma", pmcorrect.method= "rma" etc. etc. I need to know if / when was this bug fixed? (Have used eset <- rma() for analysis just recently....) Or do I have to use the eset <- justRMA (Data) command instead? Best regards Anna ********************************************************************** ********************* Anna Gustafsson Royal Institute of Technology AlbaNova University Center Stockholm Center for Physics, Astronomy and Biotechnology Department of Molecular Biotechnology 106 91 Stockholm, Sweden Phone (office): +46 8 553 783 41 Fax: + 46 8 553 784 81 Visiting adress: Roslagstullsbacken 21, Floor 3 Delivery adress: Roslagsv?gen 30B

I wouldn't necessarily classify this as a bug. More as a difference of opinion between implementers. However, it has been possible since early January to duplicate the results of expresso via the command rma() using the parameter bgversion=2 (with slight rounding differences). Or alternatively via expresso you can use bg.method="rma2" and this will duplicate the background used in rma() (exactly). Thanks, Ben > Dear all, > > I have a question considering the bug in the RMA function eset <- rma() that was highlighted (by Hu Wei) in the end of January this year. He found that the results from this rma streamline version differed from the results obtained using the individual commands: eset<. expresso(), normalize.method=quantiles, bg.method="rma", pmcorrect.method= "rma" etc. etc. > > I need to know if / when was this bug fixed? (Have used eset <- rma() for analysis just recently....) > Or do I have to use the eset <- justRMA (Data) command instead? > > Best regards > Anna -- Ben Bolstad <bolstad@stat.berkeley.edu>