Here is an error I get when running affylmGUI (and attempting RMA normalization). The errors are listed below. I am running R 1.9.1 on a Windows XP machine. I downloaded the Estrogen example .cel files and the program worked fine. When I attempted the same with .cel files I got from the contractor who does our microarray experiments, there are no error messages when the raw data is read, but the normalization step causes a bunch of downloads from the net (One is : www.bioconductor.org/CRANrepository/repdatadesc.rda but after that the new windows flash by too fast to read) and then the two error messages at the bottom of this message. If you know anyone I should contact who might be able to troubleshoot these, I would appreciate it. I am a novice at R and affylmGUI. Below is what the screen says: __________________________________________________________________ Loading required package: limma Loading required package: affy Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: tcltk Warning: ActiveTcl could not be found in the Windows Registry. Either it has not been installed or it has not been installed with sufficient privileges. affylmGUI requires the Tcl/Tk extensions Tktable and BWidget which are not distributed with R, but they are distributed with ActiveTcl. To begin, type affylmGUI() or use the pull-down menu. Searching for user-defined affylmGUI commands in C:/PROGRA~1/R/rw1091/library/affylmGUI/etc ... Loading required package: reposTools Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == "")) return(NULL) : missing value where TRUE/FALSE needed Error in assign("NormalizedAffyData", NormalizedAffyData, affylmGUIenvironment): Object "NormalizedAffyData" not found -- Aaron Hamilton, Ph.D. Genome Biology Division Biosciences Directorate Lawrence Livermore National Laboratory 7000 East Ave., L-448 Livermore, CA 94550 [[alternative HTML version deleted]]

Hi Aaron, On Mon, Feb 07, 2005 at 01:29:57PM -0800, Aaron Hamilton wrote: > Here is an error I get when running affylmGUI (and attempting RMA > normalization). The errors are listed below. I am running R 1.9.1 > on a Windows XP machine. This may be the start of your problem. The current release version of Bioconductor requires R-2.0.1. I recommend downloading and installing R-2.0.1 and then reinstalling the Bioconductor packages you need. Feel free to post again if, after upgrading, you run into similar (or different) issues. + seth

Hi, > Here is an error I get when running affylmGUI (and attempting RMA > normalization). The errors are listed below. > I am running R 1.9.1 on a Windows XP machine. I downloaded the As pointed out already, R 1.9.1 is a bit old now. It is best to use 2.0.1 (or later). One reason why people may be posting to this list using R 1.9.1 with affylmGUI or limmaGUI is because I created an installation bundle for Windows users with: R + all the Tcl/Tk extensions required by limmaGUI/affylmGUI + all the required R packages, which some users found convenient. Unfortunately, I haven't yet done this for R 2.0.x. I'm working on it, but the way I like to do it involves building R from source (on Win32), which means that all of the required tools (gcc, make, latex etc.) have to be working correctly. And currently there seems to be something wrong with my latex installation which I'm trying to fix. And even when things are working right, it still takes a while to build and test thoroughly, so for now users can just grab the limmaGUI and affylmGUI R packages from http://bioinf.wehi.edu.au/limmaGUI/ and http://bioinf.wehi.edu.au/affylmGUI/ or from Bioconductor after installing R first, rather than in a bundle. I know there are some other affylmGUI posts I haven't responded to yet. I will when I have a chance... Best wishes, James