You should be confronted with a plot similar to the above. Open in Java TreeView, click on "Analysis->Make Scatterplot." then select SPOT for the Y-axis and leave INDEX as the X-axis and click "Go!". A more mature version may one day make it into the helper-scripts package. You can use it as a starting point for your own script. Special bonus: the perl script which I used to do the coloring: With genes which I haven't made a screenshot of.
#USE APPLET VIEWER IN JAVA HOW TO#
I also have an older example set of files which show how to associate colors Open the cdt file in excel to see how it works. In practice, you would want the colors to represent some kind of biological information here, I just did something random with excel. This garish image demonstrates how you can independantly control the background and foreground colors for genes and arrays using BGCOLOR and FGCOLOR rows and columns. Your browser is completely ignoring the tag! A subset of Paul Spellman's cell cycle data was hierarchicallyĬlustered and used with the applet distribution.
These example applets display the same files as the application examples.