User guide

Differential Display and VNTRs
18-3
1. n
q
> ratio x mean and
n
q
> mean + quantity
2. n
q
< (1/ratio) x mean and
n
q
< mean – difference
ratio = 1.0 + (percentage/100)
Select the Trend button to search for increasing or decreasing gene expression,
represented by trends in normalized quantity across a band type. In Trend
mode, a linear regression of (n
q
) versus lane # 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 the Results
Bands identified either as outliers or as belonging to a trend are displayed in
white.
If a lane does not have a band assigned to a band type that is flagged as an
outlier or a trend, an empty box will be drawn at the expected location of the
band.
The Normalized Quantity command can be used to display a histogram of
normalized quantities and the mean for any matched band that you select.
Click on the button, then click on the matched band. A graph will appear on
the image with the normalized quantities of that matched band across the
entire gel.