User guide

Quantity One User Guide
14-6
If you select the No button next to the Normalize prompt, the band detection
parameters are taken as absolute values and are applied in the same way to
every lane on the image.
If you select Yes, the parameters are automatically adjusted according to the
darkness of the lane. The darkness of the lane is determined by the darkest
band in the lane. For example, suppose that all but one of the lanes on an
image contain bands with an intensity of up to 50,000 counts. In the one light
lane, the darkest band is only 25,000 counts. If normalization is turned on,
band detection will be twice as sensitive when processing the light lane,
improving the detection of faint bands.
Shadow Rejection
“Shadow bands” are common gel artifacts. Shadow bands are spaced at
tandem repeat intervals and decrease in intensity as they progress further
from a real band. The Shadows parameter is designed to limit the detection of
shadow bands (see also Band Limit, below).
If you select Reject next to the Shadows prompt, the Detect Bands function
will only find a band if it is darker than the one above it or if it is spaced
further than one tandem repeat unit from the previous band. This greatly
reduces the number of shadows identified as real bands.
If you select Accept next to the Shadows prompt, Detect Bands will not filter
for shadows.
Band Limit
If you know that all the lanes in your gel contain a specific number of bands,
you can click on the Limit button next to the Bands prompt and type in the
number of bands that you know are present. Only that number of bands will
be detected in each lane, reducing the need for later editing.
Sensitivity
The Sensitivity setting determines the minimum signal intensity in the image
that will be defined as a band. The higher the sensitivity value, the more
bands will be detected.