User Guide

Scatter Plot
After performing a pairwise comparison, the
data can be viewed as a Scatter Plot with
the log intensities for Group 1 plotted against
the log intensities for Group 2. This plot
displays the data for all of the genes and
color codes the differentially expressed
genes. The first time Scatter Plot is
selected, there may be a few second delay
due to the initial intensive calculation.
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1. Select Scatter Plot from the
Pairwise Comparison Results
page. A new window will be
displayed.
2. Clicking print plot in the blue control
box will print the scatter plot or save
it to a file.
3. The middle toggle line button
allows the user to view/hide the
identity line.
4. All the data for that comparison will
be displayed on the plot (if multiple
experiments were included for a
group, the log of the mean intensity
for the group is plotted). Red spots
represent genes that are more highly
expressed in Group 2 and green
represents genes that are expressed
at a lower level in Group 2. Gray
spots represent genes that are not
differentially expressed based on the
criteria selected for the pairwise
comparison. Note that the color
scheme of spots can be selected
within Preferences.
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