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. 2016 Dec 20;11:66. doi: 10.1186/s13062-016-0169-7

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© The Author(s) 2016

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 5 — Inter-site differential expression calls after removing unwanted variation with svaseq. We identify genes differentially expressed between samples from alternative sites. The y-axis [DEG] shows the number of differential expression calls (q<5%). Violin plots summarize the results for all possible pairs of alternative sites. Each panel shows data for a particular method of differential expression calling. Plots for various methods of expression estimation are shown along the x-axis. Colour indicates the samples compared: A-vs-C (cyan), A-vs-A (magenta), and C-vs-C. High counts in same–same comparisons reflect a lack of specificity. Note the improvements relative to Fig. 3