Supplementary information forBolstad, 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 |
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Pre-prints
PDF version gzipped Postscript version |
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Supplementary unpublished manuscripts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Arrays PDF file Bolstad, B (2001) Probe Level Quantile Normalization for High Density Oligonucleotide Array Data Unpublished Manuscript PDF file |
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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 |
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Additional Figures
Liver Dilution series boxplots Unnormalized png Quantile png Contrast based png Cyclic Loess png Scaling png Nonlinear png |
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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 |
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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 |
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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. |
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