dear list, I would like to decompose the function 'gcrma' into its individual elements using the function 'expresso'. Does anyone know which of the individual methods (i.e. background correction, pm correction, normalization and summarization) I have to use in expresso to get gcrma as a result? Thanks Tina _________________________________________________ Bettina Harr Research Group Leader Abteilung fuer Evolutionsgenetik Institut fuer Genetik Universitaet Koeln Zuelpicher Strasse 47 50674 Koeln - Germany new!!!: Tel: ++49 221 470 2324 Fax: ++49 221 470 5975

Here is one solution to do it piece by piece, although not in expresso: First, modify the gcrma function to just do the background correction. Type: > mygcrma <- edit(gcrma) and change the last line to read: return(object) Then call: >gc.affybatch <- mygcrma(raw.affybatch) and you'll get an affybatch object with GC background corrected data. You can then do quantile normalization on this (or any other affybatch) by simply calling: > gcnorm.affybatch <- normalize(gc.affybatch) To just do the summarization on any affybatch, try: gcnorm.eset <- rma(gcnorm.affybatch, background=F, normalize=F) You can also turn off background correction and normalization in expresso, but the rma routine is faster. I don't think you can turn off summarization in expresso - see ?expresso. Cheers, Jenny At 05:30 AM 11/1/2005, Bettina Harr wrote: >dear list, > >I would like to decompose the function 'gcrma' into its individual >elements using the function 'expresso'. Does anyone know which of the >individual methods (i.e. background correction, pm correction, >normalization and summarization) I have to use in expresso to get gcrma >as a result? > >Thanks > >Tina > >_________________________________________________ > >Bettina Harr >Research Group Leader >Abteilung fuer Evolutionsgenetik >Institut fuer Genetik >Universitaet Koeln >Zuelpicher Strasse 47 >50674 Koeln - Germany >new!!!: Tel: ++49 221 470 2324 >Fax: ++49 221 470 5975 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

> methods(bg.correct) [1] bg.correct.gcrma bg.correct.LESN bg.correct.mas bg.correct.none [5] bg.correct.rma bg.correct.rma2 bg.correct.shift However, the gcrma functions have been updated in the new release. You can do library(gcrma) bg.correct.gcrma <- bg.adjust.rma so that expresso can call the one defined in pacakge "gcrma". Jean On Tue, 1 Nov 2005, Bettina Harr wrote: > dear list, > > I would like to decompose the function 'gcrma' into its individual > elements using the function 'expresso'. Does anyone know which of the > individual methods (i.e. background correction, pm correction, > normalization and summarization) I have to use in expresso to get gcrma > as a result? > > Thanks > > Tina > > _________________________________________________ > > Bettina Harr > Research Group Leader > Abteilung fuer Evolutionsgenetik > Institut fuer Genetik > Universitaet Koeln > Zuelpicher Strasse 47 > 50674 Koeln - Germany > new!!!: Tel: ++49 221 470 2324 > Fax: ++49 221 470 5975 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >