Bio-Rad Quantity One 1-D Analysis Software User Manual
Page 125
Quantity One User Guide
5-8
If Normalize is turned on, Min. Density changes from an absolute value to a
percentage. This percentage is the fraction of the signal intensity of the darkest band
in the lane that will be detected as a band. For example, if the darkest band in a lane is
50,000 counts and the Min. Density is set to 25,000 counts, when you turn on
Normalize, the Min. Density will switch to 50% (i.e., a band must be at least half as
dark as the darkest band in the lane).
Noise Filter
The Noise Filter is used to minimize the number of small fluctuations in the image
(i.e., noise) that are called bands while still recognizing larger features (i.e., real
bands). This filter becomes especially important at higher Sensitivity levels.
The Noise Filter value refers to the size of the filter in pixels (e.g., a value of 2.50
equals a filter size of 2.50 x 2.50 pixels). Features smaller than the filter size will not
be recognized as bands. Entering a noise filter size of zero turns it off completely. The
default value is 4.00.
If band detection detects doublets as single bands, decrease the Noise Filter setting
and/or increase the Sensitivity.
You can also try decreasing the Size Scale parameter instead of the Noise Filter to
improve the detection of closely-spaced bands. However, if you decrease both the
Noise Filter and the Size Scale, the fuzziness around bands may be mistakenly
detected as separate bands.
Shoulder Sensitivity
Normally, band detection tries to distinguish shoulders as separate bands. When
looking at a lane trace, these bands appear as flat or gently sloping abutments to
darker, better-defined bands (i.e., there is no dip on the trace between the two bands).
Increasing the Shoulder Sensitivity will result in more shoulders being detected as
bands. Changing this setting to zero will result in no shoulders being recognized as
separate bands.
If band detection calls a doublet a single band, check the lane trace to see if there is a
dip between the peaks of the two bands. If there is no dip, increasing the Shoulder
Sensitivity value will help resolve the two bands.