Hello I normalized a data.frame with genes in rows and conditions in columns with vsn genormalized <- vsn(ge) latter I tried to get the normalized values with the following command but I didn't get the result I need genormalized$exprs NULL furthermore I would like to save the normalized expression data in a text file I am tried write.table(genormalized, file= "genormalized.txt", sep="\t") the file was like "exprs" "genenames" "1" 4.13499853 "1" "2" 3.88214458 "2" "3" 5.84832486 "3" "4" 5.72530643 "4" "5" 5.61469995 "5" "6" 5.24160113 "6" "7" 6.23749504 "7" "8" 5.10511033 "8" "9" 7.07843853 "9" "10" 5.89613219 "10" "11" 4.43254412 "11" "12" 4.90566019 "12" "13" 6.99090268 "13" "14" 7.61601114 "14" "15" 6.21445251 "15" "16" 6.15866330 "16" ...................... how can I do to obtain the data in format that i want, like a data.frame or a matrix best regards diego

diego huck wrote: > > > Hello > > I normalized a data.frame with genes in rows and conditions in columns > with vsn > > genormalized <- vsn(ge) > > latter I tried to get the normalized values with the following command > but I didn't get the result I need > > genormalized$exprs > > NULL Hi, you use the dollar sign to get list components, but the expression matrix is a slot of the exprSet and thus can be accessed by 'genormalized@exprs' or 'exprs(genormalized)' (have a look at help(exprSet) to learn about other methods). The result can be written by 'write.table', but most Bioconductor functions are able to handle 'exprSet' objects. Regards, Joern