Fig. 5
From: Effective normalization for copy number variation in Hi-C data
Normalization of T47D Hi-C data. a. Hi-C contact maps (250 Kb resolution) of the first four chromosomes of T47D cancer Hi-C sample. When looking at the 1D cis and trans profiles, we observed that ICE introduces a bias in the normalized data, therefore validating the observation made on the simulated data. We then applied the LOIC and CAIC normalizations in order to efficiently correct the data from systematic bias, while removing or keeping the CNVs effect. b. Estimatation of the copy number signal from the Hi-C data after correction and segmentation of the 1D profile. The inferred copy number signal from the Hi-C data are highly correlated with the copy number profile from Affymetrix SNP6.0 array. c. Correlation of raw and normalized contact frequencies with the copy number