Bio-Rad Quantity One 1-D Analysis Software - Manual (Page 206)

Chapter 9. Differential Displays and VNTRs
9-3
Trends
Select the Trend button to search for increasing or decreasing levels of gene
expression across samples, represented by trends in normalized quantity across lanes.
With Trend selected, a linear regression of (n
q
) versus lane number is computed for
each band type. The leftmost and rightmost lanes containing that band type are
determined. The normalized quantities for these lanes are calculated from the
regression model. If:
abs(leftmost_n
q
– rightmost_n
q
) > difference and
Max(leftmost_n
q
, rightmost_n
q
) / Min(leftmost_n
q
, rightmost_n
q
) > ratio
then the band type is flagged as a trend.
Displaying Results
Bands identified as outliers or belonging to a trend are highlighted with a white line
in the image.
If a lane is missing a band assigned to a band type that is flagged as an outlier or a
trend, the expected location of the band will be highlighted by a white box.
Use the Normalized Quantity button in the Differential Display dialog to display a
histogram of the normalized quantities and the mean quantity for a band type. Click
on the button, then click on the band. A graph will display the normalized quantities
of that band across the entire gel.
9.2 Variable Number Tandem Repeats
If your experiments involve the use of microsatellites, VNTRs, or other repeated
elements, you can calculate the number of times a repeated element occurs in a band.
Note: You must define the Standards in the gel before you can use this function (see
section 6.1, Standards).
To calculate the VNTRs in the bands in a gel, select VNTR Calculations from the
Analysis menu. (You can also select the VNTR Quick Guide from the Help menu for
guidance on analyzing gels with VNTRs.)