I am encountering trouble with the mas implementation in the affy package. > eset<-mas5(Data) background correction:mas PM/MM correction:mas expression values:mas background correcting...done. 22283 ids to be processed | | |########## Then it hangs. I let it go for about 20 minutes but nothing has happened. According to task manager, R is still functioning. Any suggestions? I get the same response when I use eset<-expresso(Data,normalize=FALSE,bgcorrect.method="mas",pmcorrect.m ethod="mas",summary.method="mas") R1.9.1 Windows XP Pro affy 1.2.64 Mike

You affy package is fairly outdated. Try upgrading this (there might be other dependencies as well). How many arrays are you trying to normalise ? IMHO, I do not think this could be a problem because ReadAffy() works, but since MAS 5.0 does not rely on other array information you could do this array by array and combine them. There is also a function called justMAS() in package simpleaffy that you might want to try out. Regards, Adai On Fri, 2004-09-10 at 14:37, Michael Barnes wrote: > I am encountering trouble with the mas implementation in the affy > package. > > > eset<-mas5(Data) > background correction:mas > PM/MM correction:mas > expression values:mas > background correcting...done. > 22283 ids to be processed > | | > |########## > > Then it hangs. I let it go for about 20 minutes but nothing has > happened. According to task manager, R is still functioning. Any > suggestions? > > I get the same response when I use > > eset<-expresso(Data,normalize=FALSE,bgcorrect.method="mas",pmcorrect .method="mas",summary.method="mas") > > > > R1.9.1 > Windows XP Pro > affy 1.2.64 > > > Mike > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >