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. 2009 Aug 31;37(19):6323–6339. doi: 10.1093/nar/gkp706

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© The Author(s) 2009. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 9. — Sensitivity/specificity (Sn/Sp) characteristics of the normalization and analyses procedures. (A) Dependence of the analysis quality of the foldness of changes in gene expression: along ordinates Fd-foldness of controlled changes of data/Fa-minimal foldness accepted for results of differential gene expression analysis/Em = 20-minimal expression above background. (B) Dependence of the analysis quality of the number of replicates. Fd/Fa/Em = 2/1.5/20. (C) Comparison of normalization methods: two-step analysis (presented above) versus Quantile normalization versus Lowess normalization. (D) Comparison of analysis methods: associative analysis—SAM with Quantile normalization—SAM with Loess normalization. Abscise—sensitivity and specificity of the analysis as described in text.