UNIT 7.9 Analyzing and Visualizing Expression Data with Spotfire
Published Online: 1 OCT 2004
Copyright © 2004 by John Wiley & Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
How to Cite
Kaushal, D. and Naeve, C. W. 2004. Analyzing and Visualizing Expression Data with Spotfire. Current Protocols in Bioinformatics. 7:7.9:7.9.1–7.9.43.
- Published Online: 1 OCT 2004
- Published Print: SEP 2004
This unit assumes the reader is familiar with the Spotfire environment, has successfully installed Spotfire, and has uploaded and prepared data for analysis. It presents numerous methods for analyzing microarray data. Specifically, the first two protocols describe methods for identifying differentially expressed genes via the t-test/ANOVA and the distinction calculation respectively. Another protocol discusses how to conduct a profile search. Additional protocols illustrate various clustering methods, such as hierarchical clustering, K-means clustering, and principal components analysis. A protocol explaining coincidence testing allows the reader to compare the results from multiple clustering methods. Additional protocols demonstrate querying the Internet for information based on the microarray data, mathematically transforming data within Spotfire to generate new data columns, and exporting Spotfire visualizations.