Hi, Iam trying to run simpleaffy. Iam running R1.9 beta with Raqua and I have installed the simpleaffy library, after I load the library I follow the vignette: > raw.data <- read.affy() and get the following error message: Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file `covdesc' Does anyone know what this means? thanks, Simon

Hi Simon, I use simpleaffy in R1.8.1, so I can only tell you what I did to load in my data. Maybe in the meanwhile somethings have changed. You need to make a tab delimited text file containing your filenames in the first column and your sample-code in the second column and name it for instance "covdesc". See the short example below: Sample-ID pat1.cel P pat2.cel P pat3.cel P cont1.cel C cont2.cel C If you read in your data using the read.affy command, the program knows which samples are "patient" samples and which samples are "control" samples. Then you should used the following to read in your data (*.cel files and the covdesc-file need to be in your working directory): >raw.data <- read.affy(covdesc="covdesc") Greetz, Rudy. -----Original Message----- From: Simon Kidd [mailto:kidd@mail.rockefeller.edu] Sent: Saturday, April 03, 2004 12:12 AM To: bioconductor@stat.math.ethz.ch Subject: [BioC] simpleaffy Hi, Iam trying to run simpleaffy. Iam running R1.9 beta with Raqua and I have installed the simpleaffy library, after I load the library I follow the vignette: > raw.data <- read.affy() and get the following error message: Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file `covdesc' Does anyone know what this means? thanks, Simon _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor