frequency of probe intensity.
Again, this graphic is interactive with the workflow sheet
and may be customized to user
preferences (Figure 4).
The ‘Sources of Variation’
plot dramatically illustrates
the major inputs that affect
variation in the experiment
It should be noticed that
the variation in a single gene
may be quickly produced by
right-clicking on the row header
and asking for the Sources
of Variation on the resulting
The two remaining obligatory genomics plots are the
Volcano plot and the hierarchical clustering heat map that will
assist in identifying significantly
regulated genes and patterns
across genes and samples (
Figures 6 & 7).
If we need to look at a
graphic of the intensity values
and distribution for a single
624 Trade Center Boulevard
St. Louis, Missouri 63005
314-878-2329; Fax: 314-275-8453
John Wass is a statistician based in
Chicago, IL. He may be reached at
gene in a sample vs. control grouping, this
is accomplished by requesting a Dot plot
of the original data (Figure 8).
In this example, it is easy to discern the
difference from the control patient to one
with Down Syndrome.
In summary, the software combines
easy-to-use statistics with interactive
graphics and is available for Windows,
Macintosh and Linux. Interested parties
should request the free two-week trial
version. Downloading and setup are quick
and easy, and the novice will find many
exciting and extremely helpful features.