The application displays the Abundance (Scaled) column and the Abundance (Grouped) column in blue, white, and red tones. For information about how the application calculates the values in these columns, see Calculating group abundances.
The application uses the settings of the 1st Fold Change Threshold, 2nd Fold Change Threshold, 3rd Fold Change Threshold, 4th Fold Change Threshold, and 5th Fold Change Threshold parameters of the Reporter Ions Quantifier node and the Precursor Ions Quantifier node to color the scaled abundance values and the ratios calculated from the abundance values shown in the Abundance (Scaled) column and the Abundance (Grouped) columns. For the ratios, the application directly uses the fold changes as thresholds for applying colors from dark blue (downregulation) to white (no regulation) to dark red (upregulation). For the scale abundance values, the application colors the values according to their deviation from 100. It calculates the thresholds of the scaled and scaled-and-grouped abundances as follows:
T is the given fold change, and 100.0 is used to scale the average of all channels to 100.0 (per file or across files).
The following figure shows the thresholds of the scaled abundance values for the default fold changes.
The following figure shows the fold-change coloring scheme for the grouped abundance and scaled abundance values.