Supplementary information for

Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003)

A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance.

Bioinformatics 19,2,pp 185-193

Pre-prints
PDF version
gzipped Postscript version
Supplementary unpublished manuscripts
Astrand, Magnus (2001) Normalizing Oligonucleotide Arrays PDF file
Bolstad, B (2001) Probe Level Quantile Normalization for High Density Oligonucleotide Array Data Unpublished Manuscript PDF file
Figures in Manuscript
All figures in manuscript Figures.tar.gz
Figure 1 Fig1.png
Figure 2 Fig2.png
Figure 3 Fig3.png
Figure 4 Fig4.png
Figure 5 Fig5.png
Figure 6 Fig6.png
Figure 7 Fig7.png
Figure 8 Fig8.png
Additional Figures
Liver Dilution series boxplots
Unnormalized png
Quantile png
Contrast based png
Cyclic Loess png
Scaling png
Nonlinear png
Comparing Ability to reduce variance using Spike-in data set
Comparing the two baseline methods png
Comparing the Complete data methods png
Comparing the Nonlinear method with complete data methods png
Comparing the Scaling method with complete data methods png
Comparing ability of complete data methods to reduce variance using Dilution/Mixture data
Liver at conc. 20
Liver at conc. 7.5
Liver at conc. 5
Liver at conc. 2.5
Liver at conc. 1.25
Central Nervous System at conc. 20
Central Nervous System at conc. 10
Central Nervous System at conc. 7.5
Central Nervous System at conc. 5
Central Nervous System at conc. 2.5
Central Nervous System at conc. 1.25
Mixture: 75% liver, 25% CNS at conc 10
Mixture: 50% liver, 50% CNS at conc 10
Mixture: 25% liver, 75% CNS at conc 10
Diagrams demonstrating M vs A and Baseline type normalization
M vs A plot indicating normalization process
Demonstration of normalization using M vs A
Demonstration of Baseline normalization The scaling method would use a straight line through the origin as the normalization curve, the non linear method uses a smooth curve.
This diagram demonstrates the class of normalizations that the Quantile normalization algorithm falls.
Contact the authors at bolstad@stat.berkeley.edu