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Figure 4 | BMC Bioinformatics

Figure 4

From: Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data

Figure 4

PCA filtering can improve fit to interaction model.A) There is an optimal number of PCs to use in reconstructing the energies of interaction δ F i,j . Shown are the Pearson correlation coefficient and reduced χ 2 of the genome-wide fits of the given data (see legend) to the model using Eq. 5 as a function of the number of PCs used in the filtering. For the energies derived from raw matrix, PC1 was excluded as it is simply a DC offset. (B, C) show the best fit results for the various datasets by chromosome. PCA filtering for the raw matrix leads to the best overall results.

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