Alternatives to Log‐Scale Data Display

Joseph Trotter1

1 BD Biosciences, San Diego, California
Publication Name:  Current Protocols in Cytometry
Unit Number:  Unit 10.16
DOI:  10.1002/0471142956.cy1016s42
Online Posting Date:  October, 2007
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Abstract

Traditional log‐scale data display of multiparameter immunofluorescence cytometry data has several perplexing intrinsic problems that are largely mitigated by recent transformation alternatives that are log‐like at the high end of the scale, near linear at the low end of the scale, and symmetrical about zero. These alternative log‐like display transformations provide a means for better interpretation and analysis of compensated data. Curr. Protocol. Cytom. 42:10.16.1‐10.16.11. © 2007 by John Wiley & Sons, Inc.

Keywords: Flow cytometry; data display; log transformation; Logicle transformation; biexponential; Hyperlog transformation; generalized log transformation; glog; compensation artifacts

     
 
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Table of Contents

  • Introduction
  • Background Information
  • Appendix: Transformation Functions
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Bagwell, B.C. 2005. HyperLog—a flexible log‐like transformation for negative, zero, and positive valued data. Cytometry A 64A:34‐42.
   Durbin, B. and Rocke, D.M. 2003. Estimation of transformation parameters for microarray data. Bioinformatics 19:1360‐1367.
   Herzenberg, L.A., Tung, J., Moore, W.A., Herzenberg, L.A., and Parks, D.R. 2006. Interpreting flow cytometry data: A guide for the perplexed. Nat. Immunol. 7:681‐685.
   Johnson, N.L. 1949. Systems of frequency curves generated by methods of translation. Biometrika 36:149‐176.
   Parks, D.R., Roederer, M., and Moore, W.A. 2006. A new “Logicle” display method avoids deceptive effects of logarithmic scaling for low signals and compensated data. Cytometry A 69A:541‐551.
   Rocke, D.M. and Durbin, B. 2003. Approximate variance‐stabilizing transformations for gene‐expression microarray data. Bioinformatics 19:966‐972.
   Roederer, M. 2001. Spectral compensation for flow cytometry: Visualization artifacts, limitations, and caveats. Cytometry 45:194‐205.
   Tung, J.W., Parks, D.R., Moore, W.A., Herzenberg, L.A., and Herzenberg, L.A. 2003. New approaches to fluorescence compensation and visualization of FACS data. Clin. Immunol. 110:277‐283.
   Zhou, L. and Rocke, D.M. 2005. An expression index for Affymetrix GeneChips based on the generalized logarithm. Bioinformatics 21:3983‐3989.
Internet Resource
  http://stat‐www.berkeley.edu/users/terry/zarray/Affy/GL_Workshop/genelogic2001.html
  Workshop Web site presentation: Munson, P.J. 2001. “Consistency” test for determining the significance of gene expression changes on replicate samples and two convenient variance‐stabilizing transformations. In Genelogic Workshop on Low Level Analysis of Affymetrix Genechip Data.
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