Tech Notes
Q. Is it possible to generate a volcano plot in GeneSpring?
A. Yes, using scripts from the Bioscript Library. A volcano plot is helpful in identifying significance and magnitude of change in expression of a set of genes between two conditions. A volcano plot displays the negative log of p-values from a t-test on one axis and the log2 of change between two conditions on the other axis on the Scatter Plot view. Use the scripts found in the Bioscript Library 2.1 (available in GeneSpring 6.2), under "Biological Queries" to generate the lists that will be used to create the Volcano Plot view.
The Bioscript Library is also available for download at http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/bioscripts.smf.
To use the scripts in GeneSpring:
- click once on this script in the Scripts folder
- enter the required inputs and click Start
- Save the lists generated
See the script notes for further explanation of functionality and additional instructions on setting Scatter Plot display options. More detailed information can also be found in the document describing the latest features in GeneSpring version 6.2, by selecting "User Manual" from the Help menu.
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