Setting
Description
Slope Thresholds Peak Start and End • Peak Start—The peak starts when the first derivative (slope of the
tangent) in the beginning of the peak signal before the inflection point
becomes equal to or exceeds the “Peak Start” value. This threshold is
set to 0 by default, which means that the peak will normally start at the
leftmost point where the slope of the tangent is closest to 0° (horizontal
line). A value other than 0 moves the peak start point toward its center.
The value entered must be non-negative.
• Peak End—The peak ends when the first derivative (slope of the tangent)
in the end of the peak signal after the inflection point becomes equal to
or exceeds the “Peak End” value. This value is set to 0 by default, which
means that the peak will normally end at the rightmost point where the
slope of the tangent is closest to 0° (horizontal line). A value other than 0
moves the peak end point toward its center. The value entered in this
field must be non-positive.
Sizecalling protocol—QC settings
Setting
Description
Size Quality
The Pass Range and the Fail Range for the SQ flag displayed in View Fragment
Results.
Results that are within the Pass range are flagged as (Pass). Results that are within
the Fail range are flagged as (Fail). Results that are between the Pass and Fail
ranges are flagged (Check).
For example, with a Pass Range of 0.75 to 1.0 and a Fail Range of 0.0 to 0.25, any
result
³
0.75 is , any result <0.25 is , and any result between
³
0.25 to <0.75 is .
How Size Quality is determined
The Size Quality algorithm evaluates the similarity between the fragment pattern for
the size standard dye specified in the size standard definition and the actual
distribution of size standard peaks in the sample, calculates an interim SQ (a value
between 0 and 1).
Assume Linearity
Defines the expected linear range. Useful in large fragment size standards where non-
linearity might be expected.
Pull-Up
The pull-up ratio and tolerance for pull-up peak identification. A pull-up peak is
identified when the peak height of the minor peak is:
•
£
X% (pull-up ratio) of the major peak
and
• Within ±Y data point (pull-up scan) of the major peak
When at least one peak is identified as a pull-up peak, the (Check) flag is displayed
for the Spectral Pull-Up quality flag in View Fragment Results.
Chapter 7
Manage library resources
Sizecalling protocols library (primary analysis—fragment)
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3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1
