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. 2007 Aug 7;35(15):e99. doi: 10.1093/nar/gkm549

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© 2007 The Author(s)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/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 2. — Properties of the nearest-neighbor strategy. (A) Feature pairs with several mismatches are weak predictors of signal. All possible pairs of features from a single tiling microarray design were analyzed. The average correlation coefficients (blue circles, left axis) and number of pairs contributing to those averages (orange bars, right axis) are plotted for all possible number of mismatches. (B) Expected number of mismatches between a tile and its nearest-neighbor probe sequence. For a number of mismatches, k, the expected number of features having k or fewer mismatches to any 25nt tile is plotted. These expectations are plotted for array designs having 10⁵, 10⁶, 10⁷ and 10⁸ features. The value of k for which a series crosses unity on the y-axis represents the expected number of mismatches between a tile and its nearest-neighbor probe sequence. (C) Detail of this cross-section.