Dear Bio.C, I want to use gcrma function, to get expression from a genechip experiment, but I don't want to use any normalization methods. I tried to use expresso this way, > bgcorrect.methods<-c(bgcorrect.methods,"gcrma") > n<-expresso(r, bgcorrect.method="gcrma", normalize.method= FALSE, pmcorrect.method="pmonly", summary.method="medianpolish") background correction: gcrma normalization: FALSE PM/MM correction : pmonly expression values: medianpolish background correcting...Error in bg.correct(afbatch, method = bgcorrect.method) : Unknown method (cannot find function bg.correct.gcrma ) but as you can see it didn't works... do ou have any other suggestion? Claudio Isella

The bg.adjust.gcrma function is not available in the previous releases. We are going to include that in the next release. The devel version has this function and you can try that. We are testing the devel version now. Just notice currently the devel version has default "fast=FALSE" unlike the previous releases. You will need to specify "fast=TRUE" if you want to stay with the previous default settings. best, Jean On Tue, 30 Aug 2005, claudio.is at libero.it wrote: > Dear Bio.C, > > I want to use gcrma function, to get expression from a genechip experiment, but I don't want to use any normalization methods. > > I tried to use expresso this way, > > > bgcorrect.methods<-c(bgcorrect.methods,"gcrma") > > n<-expresso(r, bgcorrect.method="gcrma", normalize.method= FALSE, pmcorrect.method="pmonly", summary.method="medianpolish") > background correction: gcrma > normalization: FALSE > PM/MM correction : pmonly > expression values: medianpolish > background correcting...Error in bg.correct(afbatch, method = bgcorrect.method) : > Unknown method (cannot find function bg.correct.gcrma ) > > but as you can see it didn't works... > > do ou have any other suggestion? > > Claudio Isella > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Dear Claudio If you type > gcrma in your R prompt you will see the code of the gcrma wrapper function. Note that in the last line there is a call to the 'rma' function. You just need to add as an option 'normalize=FALSE' there. So you can just copy and paste the code into a text editor. Rename the function (for instance: mygcrma), modify the last line as I told you, and source it into R. Ariel./ On August 30, 2005 04:21 am, claudio.is at libero.it wrote: > Dear Bio.C, > > I want to use gcrma function, to get expression from a genechip experiment, > but I don't want to use any normalization methods. > > I tried to use expresso this way, > > > bgcorrect.methods<-c(bgcorrect.methods,"gcrma") > > n<-expresso(r, bgcorrect.method="gcrma", normalize.method= FALSE, > > pmcorrect.method="pmonly", summary.method="medianpolish") > > background correction: gcrma > normalization: FALSE > PM/MM correction : pmonly > expression values: medianpolish > background correcting...Error in bg.correct(afbatch, method = > bgcorrect.method) : Unknown method (cannot find function bg.correct.gcrma ) > > but as you can see it didn't works... > > do ou have any other suggestion? > > Claudio Isella > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339