UNIT 7.9 Analyzing and Visualizing Expression Data with Spotfire

  1. Deepak Kaushal,
  2. Clayton W. Naeve

Published Online: 1 OCT 2004

DOI: 10.1002/0471250953.bi0709s7

Current Protocols in Bioinformatics

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.

Author Information

  1. St. Jude Children's Research Hospital, Memphis, Tennessee

Publication History

  1. Published Online: 1 OCT 2004
  2. 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.