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. 2018 Nov 26;19:233. doi: 10.1186/s12931-018-0932-7

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© The Author(s). 2018

Open AccessThis 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. 1 — Volcano plots obtained with four pipelines. Pipelines: a EdgeR glmLRT normalization, b EdgeR glmLRT normalization with RUV, c EdgeR glmQLF normalization with RUV, d DESeq Wald normalization with RUV. Differentially expressed genes between control subjects and IPF patients are shown in blue (FDR q < 0.05). The upregulated genes associated with pattern-recognition receptor (PRR) molecular function are highlighted in red