What are the baseline and threshold values?
The baseline and threshold values are used to exclude or filter out low intensity, poor-quality data before analysis. Baseline value is a number (such as 200, 500) that you set to filter out low intensity spots. For a spot with signal intensities in both channels below the user defined baseline value (before background subtraction), this spot will be be filtered out (filtering) leaving those features with signal greater than baseline value in at least one channel. A spot whose intensities in only one channel is below the user defined baseline value (before background subtraction) will be increased to this baseline value (scaling). The threshold value (T-value) is also a number (such as 1, 2, or 3) that you can set to filter out “noisy” spots. Based on the T-value, GPAP will calculate a dynamic value for each spot (Feature Background Intensity + [T-value * Background Standard Deviation]) and spots with intensities below the threshold in both channels (before background subtraction) will
