Files are plotted in Excel with X and Y coordinates for each point/sample on the MDS plots. These plots provide information about how closely or diffusely groups of samples cluster together, viz. gene expression. A useful primer on the principle of multidimensional scaling can be found here.
Information about samples (tumor subtype, whether primary tumor or matched normal etc.) are also provided as needed.
The tumor types below include tumor subtypes as described in Table 1, e.g. the file with Breast Cancer IDC includes Her2+, Hormone Receptor+, Triple + and Triple - subtypes of BRCA IDC.