Getting Started: Loading Expression Data
Gene expression can be loaded into Genomica in two different ways:
Tab-delimited file: These files have a .tab extension. The first row is a header row, where the names of the arrays/experiments are specified from column 3 and on. The second row and on specify expression data for each gene, where the first column is the unique identifier of each gene, the second column specifies the name and the description of the gene, where the name and description are separated by " - " (the surrounding spaces are important), and column 3 and on specify the expression data for the gene across all experiments. The file linked here contains a sample file with eight genes and 7 arrays.
Genomica formatted file: These files have a proprietary format with the extension '.gxp' and can be used to store the results of complex analyses. They serve as the main file format in Genomica, where a single gxp file can store within it additional annotation files and analyses. The file linked here is the gxp formatted file for the sample tab-delimited file above.
You can load expression data from the File -> Open menu (for .tab files you must select the tab extension). After loading any of the above sample files, the cluster view should be similar to the following:
Note that you can control various properties of this view, including the color and maximum intensity of the induced and repressed expression values, the color for missing values, the width and height of the pixels, and the color and width of padding lines on top of the expression data. Finally, the expression data can also be clustered using the clustering buttons. All of these controls appear in the control panel on the left.