Hi, I figured out how to compute RMA expression measure using expresso(): eset<-expresso(Dilution, bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish") But, how do I compute MAS5.0 and dChip expression measure using expresso()? The help page of expresso() doesn't show all the available options for arguments bgcorrect.method, normalize.method, pmcorrect.method and summary.method. And where can I find all the available options for these argument? Thank you, John

Hi John, You can use mas5 instead. Alternatively, by entering mas5 you will see the code for it (including the appropriate call to expresso). Regards, Moshe. --- On Wed, 23/6/10, array chip <arrayprofile at="" yahoo.com=""> wrote: > From: array chip <arrayprofile at="" yahoo.com=""> > Subject: [BioC] MAS5.0 and dChip syntax using expresso() > To: bioconductor at stat.math.ethz.ch > Received: Wednesday, 23 June, 2010, 9:51 AM > Hi, > > I figured out how to compute RMA expression measure using > expresso(): > > eset<-expresso(Dilution, bgcorrect.method="rma", > normalize.method="quantiles", pmcorrect.method="pmonly", > summary.method="medianpolish") > > But, how do I compute MAS5.0 and dChip expression measure > using expresso()? The help page of expresso() doesn't show > all the available options for arguments bgcorrect.method, > normalize.method, pmcorrect.method and summary.method. > > And where can I find all the available options for these > argument? > > Thank you, > > John > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >