Here is what I run: > Data <- ReadAffy() > eset <- expresso(Data, normalize=FALSE, bgcorrect.method="mas",pmcorrect.method="mas",summary.method="mas") The method "mas" should be MAS5 method as it says in the introduction document. But the output file only has 2 columns: qualifier names and numerical signal values. How do I get absent/present decision calls? Dapeng

On Fri, 16 May 2003 Dapeng.Xu@aventis.com wrote: > Here is what I run: > > > Data <- ReadAffy() > > eset <- expresso(Data, normalize=FALSE, > bgcorrect.method="mas",pmcorrect.method="mas",summary.method="mas") > > > The method "mas" should be MAS5 method as it says in the introduction > document. the code was written using mas a short-hand for MAS 5.0. > > But the output file only has 2 columns: qualifier names and numerical signal > values. > > How do I get absent/present decision calls? expresso returns expression values not present absent calls. present/absent calls, as implemented by Affymetrix is not currently implemeneted. however, its relatively easy to code if you have the MAS 5.0 manual. > > Dapeng > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >