I am trying to work through the Vignette entitled "textual description of affy" and am encountering errors. Everything is fine until I reach page 10, the first command, at which point I received several erros that I have worked through to give me the following command: > eset<-expresso(Data,normalize.method="qspline",bgcorrect.method="rma", summary.method="liwong") I am now getting the following error and am unsure how to fix this: Error in expresso(Data, normalize.method = "qspline", bgcorrect.method = "rma", : pmcorrect.method missing If I was not supposed to "correct" the command this way, how should I have worked through the errors ("unused argument(s) (bg.method ...)?" and " Object "affybatch" not found"). I have used "Update packages from Bioconductor" and "Update packages from CRAN" to no avail. Any help would be appreciated. Michael Barnes

That looks like an error in the vignette which will be corrected. Usually with expresso() you need to specify a method for each of the four steps. In this case it looks like the example forgot to include the pmcorrect.method. You should find something like eset<-expresso(Data,normalize.method="qspline",bgcorrect.method="rma", pmcorrect.method="pmonly",summary.method="liwong") should work fine. Thanks, Ben On Tue, 2003-06-24 at 06:29, Michael Barnes wrote: > I am trying to work through the Vignette entitled "textual description > of affy" and am encountering errors. Everything is fine until I reach > page 10, the first command, at which point I received several erros that > I have worked through to give me the following command: > > > > eset<-expresso(Data,normalize.method="qspline",bgcorrect.method="rma ",summary.method="liwong") > > I am now getting the following error and am unsure how to fix this: > > Error in expresso(Data, normalize.method = "qspline", bgcorrect.method > = "rma", : > pmcorrect.method missing > > If I was not supposed to "correct" the command this way, how should I > have worked through the errors ("unused argument(s) (bg.method ...)?" > and " Object "affybatch" not found"). I have used "Update packages from > Bioconductor" and "Update packages from CRAN" to no avail. > > Any help would be appreciated. > > Michael Barnes > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad