affylmGUI is a Graphical User Interface for analysis of Affymetrix microarray data, using Gordon Smyth's limma package (Linear Modes for MicroArray data). limma and affylmGUI are both R packages. The limma package offers R users a command-line interface to state-of-the-art techniques for linear modelling of microarray data and for identifying differentially expressed genes. The affylmGUI package, while not as powerful as limma to the expert user, offers a simple point-and-click interface to many of the commonly-used limma and affy functions. To use the affylmGUI package, you need to have R 1.8.1 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows/Linux or Fink Tcl/Tk for MacOSX (X11)) and the limma, affylmGUI, tkrplot R packages. The affyPLM (Bioconductor), R2HTML (CRAN) and xtable (CRAN) packages are recommended. The limma and affyPLM packages are available on Bioconductor (Click on Release 1.3 packages), the affylmGUI package is available here, and the other packages are available from CRAN. affylmGUI has been succesfully tested on Windows 2000, Windows XP, and Red Hat Linux, and on Mac OSX with X11.