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Hi Sally -- have a look at the vignette 'An introduction to Biobase and ExpressionSets', section 4.1, if you haven't already. > library(Biobase) > openVignette() The vignette is also available as 'ExpressionSetIntroduction.pdf' at http://bioconductor.org/packages/2.1/bioc/html/Biobase.html >From what you've written, myexprdata needs to be a matrix, perhaps > myexprdata <- as.matrix(myexprdata) will work. If phenotypicdata is a data.frame with the correct information, then the next step should be > adf <- new("AnnotatedDataFrame", data=phenotypicdata) > eset <- new("ExpressionSet", exprs=myexprdata, phenoData=adf) The vignette goes through additional details. There are example files in Biobase that the vignette points you to if you need some more help. If you run in to problems, you'll need to provide a bit more information, especially the error message(s) that you encounter. Toward the end of the vignette, in section 4.5, there's a 'minimal' expression set, with just > new("ExpressionSet", exprs=myexprdata) and that might be a good place to start if you're frustrated. Please also include the output of > sessionInfo() so that others can see what version of R and Biobase you're using -- hopefully you're using a recent version of R (2.6.0 or 2.6.1) and you've either used biocLite to install Biobase, and / or the instructions at http://www.bioconductor.org/download for information on updating packages. Hope that helps, Martin Sally <sagoldes at="" shaw.ca=""> writes: > I have read in my data with the following: > > myexprdata<-read.table("exprMatrix.txt", header=TRUE) > phenotypicdata<-read.table("phenotypicdata.txt",header=TRUE) > > but despite working on it all day I haven't yet been able to create an exprSet. Could someone help me? Please!!! > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793