Bio-Rad Firmware & Software Updates - Manual (Page 109)

Gene Expression Analysis
98
The clustergram image depicts relative expression of a sample or target as follows:
• Upregulation (red). Relatively higher expression
• Downregulation (green). Relatively lower expression
• No regulation (black)
• No value calculated (black with a white X)
The lighter the shade of color, the greater the relative expression difference. If no normalized
Cq value can be calclulated the square will be black with a white X.
On the outer edges of the data plot is a dendrogram, which indicates the clustering hierarchy.
Targets or samples that have similar expression patterns will have adjacent branches while
those with dissimilar patterns will be more distant.
Settings
The following can be set:
• Cluster by. Targets, Samples, Both, or None can be selected
• Size. Image size can be adjusted using the slider to alter the degree of chart
magnification for easier visualization
• Split out replicates. This option shows values for the individual replicates
TIP: The color scheme for clustergram, scatter plot, volcano plot, and heat map
can be changed from the default Red/Green to Red/Blue by selecting this option
from the right-click menu on any of these charts.
Right-Click Menu Options
Right-click on the clustergram to select the items shown in Table 38.
Table 38. Right-click menu items.
Data Spreadsheet
The spreadsheet lists the target, sample, and normalized expression. Click the check box
adjacent to a target to include or exclude it from the clustergram. Select chart options by right-
clicking.
Scatter Plot
The scatter plot shows the normalized expression of targets for a control versus an
experimental sample.
The plot image shows the following changes in target expression based on the threshold set:
Item Function
Copy Copy the chart to a clipboard
Save Image As... Save the graph in the chart view as an image file. The file type
options are PNG, GIF, JPG, TIF, or BMP. The image resolution
will be the same as the computer display
Print... Print the chart view
Color Scheme Choose Red/Green or Red/Blue for the chart colors