Hi, Bioconductors: I want to creat a exprSet class, it combines expression data and phenotype data together. expression data is a matrix with columns representing patients and rows respresent genes. The phenoData contains the patient level, the column represent level and the rows represent patients. The format of the two datasets are shown below: The gene expression data: P01 P02 P03 P04 P05 P06 P07 P08 P09 P10 P11 P12 P13 P14 P15 1007_s_at 1336.97 1244.81 1242.41 1514.92 1531.80 1244.61 1030.43 967.83 866.32 1253.16 1218.51 1518.09 1401.07 1281.88 1438.96 ........ the phenotype data: Patient Phenotype P01 Def P02 Def P03 Def ...... My codes: >x<-read.table("exprstry.txt", header=TRUE) >y<-read.table("phenotype.txt", header=TRUE) >eset<-new('exprSet', exprs=x, phenoData=y) Error in validObject(.Object) : Invalid "exprSet" object: 1: Invalid object for slot "exprs" in class "exprSet": got class "data.frame", should be or extend class "exprMatrix" Invalid "exprSet" object: 2: Invalid object for slot "phenoData" in class "exprSet": got class "data.frame", should be or extend class "phenoData" Why it doesn't work. Thanks. Yours John