UNIT 7.8 Loading and Preparing Data for Analysis in Spotfire

  1. Deepak Kaushal,
  2. Clayton W. Naeve

Published Online: 1 SEP 2004

DOI: 10.1002/0471250953.bi0708s6

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Kaushal, D. and Naeve, C. W. 2004. Loading and Preparing Data for Analysis in Spotfire. Current Protocols in Bioinformatics. 6:7.8:7.8.1–7.8.25.

Author Information

  1. Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee

Publication History

  1. Published Online: 1 SEP 2004
  2. Published Print: JUN 2004


This unit strictly focuses on data preparation within Spotfire. Microarray data exist in a variety of formats, which often depend on the particular array technology and detection instruments used. The first protocols in this unit describe loading Affymetrix and GenePix data into Spotfire. Once the data are loaded, it is necessary to filter and preprocess the data prior to analysis. Subsequently, the data transformation and normalization techniques presented here, are critical to correctly performing powerful microarray data mining expeditions. These steps extract or enhance meaningful data characteristics and prepare the data for the application of certain analysis methods such as statistical tests to compute significance and clustering methods—which mostly require data to be normally distributed. The unit outlines several methods for normalizing the data within an experiment and between multiple experiments.