Main Window
The GenEx main window is divided into sections and this is what it looks like as a whole.
The top left contains the main menu and buttons to edit and load a file, buttons to delete, import, and export a project, as well as buttons to open a chart, bring the Control panel to the front and to get information about your gene from online databases. Edit file is used to open a data file for editing, such as irreversible scaling or normalization, in the Data editor. Load file loads a data file into a new project so that it can be used in the analyses. Delete project removes the active project from the Control panel, but does not delete it from your computer.
Import project opens a project into the Control panel, and Export project saves the active project. A project includes all the files and settings you have made, such as associated data files, data sets, groupings, coloring of groups/samples etc.
Several analyses produces charts that can be saved, and one way of opening these charts is to press the Open chart button. The Control panel is where you control your project, data files, data sets, as well as all analyses. It can be brought to the front by pressing the Bring control panel to front button. The Gene Info button lets you search the databases Entrez and/or Ensembl for information about the genes in the active data file.
If several data files have been loaded into a data set in a project, you can easily switch between the data files in the drop-down list at the top middle. The active data file is the data that the plots and analyses will be based on.
The top right of the main window contains buttons to transpose the data, view and manage the data, as well as several plotting options. Transposing the data means that the first row becomes the first column and so on. This transformation of the data is reversible, and the data is returned to its original form if the button is pressed a second time. When the View data button is pressed, you get to see the managed data in a sheet. All reversible scaling, transpositions, and inactivation of columns/rows are shown, but the data cannot be edited in the sheet. To edit the data file, select Edit file in the File menu in the main window. The Manage data button opens the Data manager where you can activate/deactivate rows and columns in the data, define groups of samples, as well as coloring of samples or genes. The settings you define in the Data manager will be stored in a data set. You can have several data files in one data set, or several data sets containing the same data file.
The four plotting buttons lets you visualize the data in basically the same way but with different graphics. 2D plot is a scatter plot which plots the rows dependent on the columns, so that the x-axis is on categorical scale. 2D line plot does the same but connects the dots with a line for each row, and 3D line plot is the same as a 2D line plot but with 3D graphics. The bar plot illustrates each data point with a bar, and data points from the same column are grouped together. A box and whiskers plot illustrates the median, upper and lower quartiles, maximum and minimum values, and outliers for each column, in a plot.
Below the buttons described, you will find tabs that contain the analyses available. Several analyses might be available on each tab.
The main window also contains the Control panel. This is where projects, data sets and data files are handled, as well as the analyses.
At the bottom of the main window is the status bar. Here you can easily see which project and data set that is active, if the data is transposed, the dimension of the active data as well as the dimensions of all data in the data file.
