sampleNames is not a variable that can be passed to justRMA (see ?justRMA for the help file). If you want the column names to be the cel file names, just do Data1 <- justRMA ( phenoData=pD1) exprs2excel(Data1,"spreadsheetname.xls") You will have to hand enter 'Gene Names' in the first cell of the spreadsheet. You could probably hack the code for read.table() to get it to put 'Gene Names' in the spreadsheet automatically, but I doubt it would be worth the effort. Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Joshi, Nina (NIH/NCI)" <joshini@mail.nih.gov> 03/31/04 03:38PM >>> I am uploading cel files with the command justRMA. I create a phenoData file first using: pD1 <- read.phenoData(filename="phenodata.txt, header = T, sep="\t') note: phenodata.txt is a text file with variables in columns and samples number and/or names in rows. The output file appears to have the correct number of cases (133) and variables (20) Then I create a file, x, that has all the CEL file names. Then I attempt to create a Affybatch using justRMA: Data1 <- justRMA (sampleNames=x, phenoData=pD1) The output file, a matrix, opened in excel has the correct number of CEL files listed in columns (133 cases) and the correct number of genes listed in rows, but the columns are shifted to the left. They are numbered x1, x2, x3...with the first column, the gene name, numbered as x1 and the last column, data from a CEL file, left blank. I want the columns named with CEL file names and the first column names "gene names". What is the code to do this? Thanks, Nina Nina Joshi, PhD NIH/NCI/ Genetics Branch National Naval Medical Center, Bldg. 8, Rm. 5101 8901 Wisconsin Ave. Bethesda, MD. 20889-5101 (301) 435-5436 - phone (301) 496-0047 - fax [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor