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. 2015 Apr 2;4(2):162–187. doi: 10.3390/microarrays4020162

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© 2015 by the authors; licensee MDPI, Basel, Switzerland.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).

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Overlap of significant antigens derived from class comparison analysis (p < 0.001) with different normalization methods for the SCLC group. Data was analyzed unnormalized, quantile normalized (QN), DWD-adjusted, and ComBat-adjusted. Significant antigens of SCLC versus controls from (a) single run analysis (“run-wise” analysis) and (b) analysis of two combined experimental runs (“cross-run” analysis). Highest numbers of overlapping antigens are observed between QN and ComBat (318 and 256, respectively). (c) Excerpt of Supplementary Figure S4 showing relative overlaps (% representing the intersections of findings depicted in Figure 5a,b) of all class comparison analyses results between quantile normalization and ComBat adjustment.