You access this mode by clicking the “3D” button in a Result Tab.

    Unlike the clustering tool of ArrayMiner, this view does not show the genes in the experiment space, but rather the samples (experiments) in the marker genes space.

    Each class has a unique color. You can use the various checkboxes to customize the rendering. To select a particular sample switch the table in the bottom of the window to "Experiments", and click the appropriate line. If a sample is misclassified, as shown in the figure on the left, a small colored panel is attached to it, showing the color of the class it has been assigned to (in the figure on the left, the targeted sample should belong to the purple class, but has been assigned to the green class instead).

    The 3D cube and all the data displayed inside can be easily rotated in real time into any viewing angle by simply clicking the mouse inside the cube and dragging it in the desired direction. The view can be zoomed in or out with the mouse wheel.

    If you are not in PCA mode, you can directly select a gene to become an axis, by right-clicking the appropriate line in the table in the bottom of the window (the table must be in Markers mode) and selecting “Set this gene as x,y or z axis”.

    If you are in PCA mode, you can change the axes by clicking on the buttons placed in the upper right part of the window.

    You can highlight a particular experiment by turning the bottom table to the "Experiments" mode by clicking on the "Experiments" button on the top of it, and choosing a particular experiment by clicking in it. The experiment will be targeted in the 3D mode as shown in the above figure.