Fold Changes, Log Ratios, Background Correction, Shrinkage Estimation, and Variance Stabilization

Part of the Use R! book series (USE R)


Microarray data are affected by experimental variability, which is a combination of systematic and stochastic variability. The basic task of microarray preprocessing is to extract quantities of interest from the data while correcting for systematic variations and controlling the stochastic variability. In this exercise we explore the concepts of (log-)ratios, the role of background correction, the idea of shrinkage estimation, and the generalized logarithm. Some tools for this are provided by the package vsn.


Background Correction Stochastic Variability Shrinkage Estimation Empirical Standard Deviation Unexpressed Gene 


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Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  1. 1.Wellcome Trust Genome CampusEuropean Bioinformatics Institute, EMBL Outstation HinxtonCambridgeUK

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