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. 2011 Dec 17;12:480. doi: 10.1186/1471-2105-12-480

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Copyright ©2011 Risso et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Yeast dataset: GC-normalized log-fold-change vs. GC-content. Stratified boxplots of count log-ratio vs. GC-content, for the two YPD cultures/library preparations of Figure 2, Panel (b), for four within-lane GC-content normalization procedures. Panel (a): Regression normalization using loess. Panel (b): Global-scaling normalization using the median. Panel (c): Full-quantile (FQ) normalization. Panel (d): Conditional quantile normalization (CQN). The first three within-lane procedures were followed by FQ between-lane normalization; CQN includes its own between-lane normalization. All methods seem to effectively reduce the dependence of fold-change on GC-content (compared to Figure 2, Panel (b)).