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. 2018 Jul 24;5:180136. doi: 10.1038/sdata.2018.136

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Copyright © 2018, The Author(s)

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article.

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(a) The effect of batch effect removal is clearly demonstrated using the plotMDS function. (b) The MDS plot of our merged microarray dataset shows a clear separation between different disease phenotypes (925 primary NSCLC tumors: red; 193 non-tumors: green). (c) The merging effect of the ComBat technique on the fRMA-normalized data is illustrated using the plotRLE function. (d) The local effect of the ComBat method at the gene-level is demonstrated using the plotGeneWiseBoxPlot function. A1BG gene was selected for the demonstration purpose.