Hello, here are some more details on how I got the errors below: I am running AffylmGUI with the latest version of R (2.0.1) on a Windows XP machine. As far as I can tell I have all the packages and activeTcl re-installed, although perhaps something is missing? I have .cel files for affymetrix data, just simple comparisons (a control vs. a manipulated cell sample), which I load into AffylmGUI. The step where I load the raw data (select targets file) seems to work OK, and now do does the RMA normalization step. I can get the chart (normalized intensity box plot) of the normalized data and it looks OK. But when I get to the 'Linear model: compute contrasts' step and beyond, I get the error messages at the bottom. Here is the transcript from the R window > library(affylmGUI) Loading required package: limma Loading required package: tcltk Loading required package: affy Loading required package: Biobase Loading required package: tools 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: reposTools ActiveTcl was found in the Windows Registry (for LOCAL_MACHINE), installed in C:\Tcl This directory will be added to the Tcl search path to enable affylmGUI to find the Tktable and BWidget extensions. To begin, type affylmGUI() or use the pull-down menu. Searching for user-defined affylmGUI commands in C:/PROGRA~1/R/rw2001/library/affylmGUI/etc ... Background correcting Normalizing Calculating Expression Loading required package: tkrplot Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users [1] "Attempting to download hgu133a from http://www.bioconductor.org/data/metaData/" [1] "Download complete." [1] "Installing hgu133a" [1] "Installation complete" Loading required package: hgu133a [here I attempted to get the M-A plot anyway, and it was abnormal] Errors from linear model/compute contrasts step Error in inherits (x,"data.frame"):subscript out of bounds Error in assign ("fit", fit, affylmGUIenvironment):Object "fit" not found Error in get(x,envir,mode,inherits):variable "fit" was not found (Then window to pick contrasts) Error in NCOL(fit$coefficients):object "fit" not found Error in min(contrastsFit$df):object "contrastsFit" not found Error in try(expr,TRUE):Object"ebayesAvailable" not found -- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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]]