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. 2014 Sep 19;3:175. Originally published 2014 Jul 30. [Version 2] doi: 10.12688/f1000research.4680.2

PMC4176427.1; 2014 Jul 30
PMC4176427.2; 2014 Sep 19

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Copyright: © 2014 Fortin JP et al.

This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

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Figure 2. — The interface shows an example interactive visualization of batch effects and quality control (TCGA head and neck squamous cell carcinoma, HNSCC dataset). The interface is divided into a user menu and a plotting area. ( a) A menu containing a number of user-settable visualization parameters. The “phenotype” is set to “plate” which makes the color scheme reflect batch. The four plots ( b– e) are interactive and react simultaneously to the user mouse clicks, so that samples selected on one plot are immediately highlighted on the additional plots. The solid lines in black represents the sample(s) currently selected by the user and match the dot circled in black on ( b, c). The dashed lines in black represents another sample, previously selected by the user and match the black dot without the circle. ( b) Average negative control probes intensities; ( c) the median intensity of the M channel against the median intensity of the U channel; ( d– e) M-value densities for Infinium I probes before and after functional normalization.