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Abstract

Preprocessing of two-color spotted arrays can be broadly divided in two main categories: quality assessment and normalization. In this chapter, we will focus on functions from the arrayQuality and marray packages that perform these tasks. The chapter begins by describing various data structures and tools available in these packages for reading and storing primary data from two-color spotted arrays. This is followed by descriptions of various exploratory tools such as MAplots, spatial plots, and boxplots to assess data quality of an array. Finally, algorithms available for performing appropriate normalization to remove sources of systematic variation are discussed. We will illustrate the above-mentioned functions using a case study.

Keywords

Background Intensity Target Information Diagnostic Plot Limma Package Color Palette 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • Y. H. Yang
  • A. C. Paquet

There are no affiliations available

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