Getting Started
When you open GenEx, the first thing you will see is the main window including the Control panel. The Control panel is a central part of the program where all projects, data sets, data files, as well as analyses are handled.
If you do not already have data ready for analyses, you can use the Data editor in GenEx or another program such as Microsoft Excel, to arrange your Cq values in. The Data editor is opened by selecting Data editor in the Tools menu at the top of the main window. Arrange the data so that columns represent genes and rows represents samples. Use the first column to index the samples and the first row to index the genes, so that each column and gene label is unique. Additional classification columns can be added for classification or normalization of the data. These extra columns are distinguished by having # preceding the label. In the example below #Total RNA indicates the amount of total RNA used to prepare the different samples, and #Class indicates which group the sample belongs to. Samples can e.g. be divided into groups such as healthy/sick, untreated/treatment1/treatment2 etc. Samples that belong the same group have the same value in the classification column. The cell A1 is used to label the experiment.
When the data has been edited it can be saved either as an Excel sheet (.xls, .xlsx), comma or tab separated text files (.csv, .txt), or as a MultiD file (.mdf). The latter file format is preferred for larger data files, because mdf-files are read and stored much faster than e.g. Excel files.
If you already have data but it requires pre-processing, import it to the Data editor by selecting Edit file in the File menu. You can also open the Data editor by selecting Data editor in the Tools menu and then either Open in the Data editors File menu, or copy-paste the data from a spread sheet to the Data editor. If the data is already pre-processed you can simply drag-and-drop the file onto the GenEx main window, or press the Load file button in the File menu of the main window. When the data i loaded into the Control panel you are ready for the analyses.
Warning: Each column and gene label should be unique before the data is submitted to plots or analyses!