Applied Biosystems 3500 User Manual

Review normalized data
Normalization corrects for instrument, capillary, and injection variability. When
specied in the primary analysis protocol, the software calculates a normalization
factor for each sample. The normalization factor is used as a multiplier to adjust the
peak height of the sample peaks relative to the GS600 LIZ
™
V2 size standard peaks.
A sample is normalized if it is collected with a normalization size standard (specied
in the primary analysis protocol [sizecalling or QC] in the assay).
Note: If the Sizing Quality is , normalization is not applied, even if the
Normalization Factor is within the normalization range. Ensure that y
ou use the
normalization size standard appropriate for your application.
To normalize, the software:
1. Determines if the data was collected on the 3500 instrument.
2. Determines if the sample was collected with a normalization size standard
denition le (normalization is enabled).
3. If normalization is enabled, the software calculates a Normalization Factor for
the sample using multiple size standard fragments. The Normalization Factor is
calculated by dividing the Normalization Target by the observed average peak
height of the size standard fragments in the samples.
4. Compares the sample Normalization Factor to the thresholds (set in the
instrument protocol).
5. If the calculated Normalization Factor is within the Normalization Factor range,
multiplies the peak heights of the sample by the calculated Normalization Factor.
6. If the calculated Normalization Factor is outside the Normalization Factor range,
multiplies the peak heights of the sample by the maximum or minimum
Normalization Factor threshold seing (for example, if the Normalization Factor
range is 0.3 to 3.0 and the calculated Normalization Factor is 5, the software
applies a Normalization Factor of 3.0).
7. Indicates the normalization state of the sample in the Normalization Limit
column in the Samples View.
If normalization is applied in the 3500 Series Data Collection Software 3.1, the
calculated Normalization factor is stored with the raw data and is applied to the raw
data in the GeneMapper
™
Software 5 and the GeneMapper
™
ID-X Software v1.2 or
later secondary analysis software. You can turn normalization o and on in the
analysis method used in the GeneMapper
™
Software 5 and GeneMapper
™
ID-X
Software v1.2 or later secondary analysis software. If normalization is not applied in
the 3500 Series Data Collection Software 3.1 (either a normalization size standard was
not used, or Sizing failed
), normalization cannot be applied in the secondary
analysis softw
are.
How
normalization is
applied
Normalization
f
actor in
secondary
analysis
Chapter 5 Review fragment/HID analysis results
Review normalized data
5
96
3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1

Applied Biosystems 3500 Specifications

General

Number of capillaries	8
Capillary Length	50 cm
Laser	Solid-state laser
Instrument Type	Capillary electrophoresis system
Technology	Capillary Electrophoresis (CE)
Weight	95 kg
Power Requirements	100–240 V