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. 2009 Oct 23;38(1):e4. doi: 10.1093/nar/gkp853

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© The Author(s) 2009. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 7. — (A–C) Density contours of scatterplots comparing expression measures obtained by MMBGX, RMA and PLIER. Separate contours are plotted for multi-mapping (red) and non-multi-mapping (black) probesets. Both RMA and PLIER have a tendency to overestimate expression values for multi-mapping probesets relative to MMBGX, as they ignore the fact that some probes map to multiple regions on the genome. There is no perceptible difference in the plots comparing RMA with PLIER between multi-mapping and non-multi-mapping probesets. This is because neither method takes into account the multi-mapping structure of the chips.