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Fig. 7 | BMC Bioinformatics

Fig. 7

From: Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software

Fig. 7

Comprehensive comparison of the pre-processing pipeline. Histogram of `A MAE` (`A MAE`: Mean Absolute Error on estimated A, the matrix of cell proportions) for 10 D matrices (mean value of 10 random noises applied on D) computed from 10 random A. Each color represents a different method. Error bars represent standard deviation on 10 random noises. RFE stands for RefFreeEWAS, MDC for MeDeCom and EDec for EDec stage 1. The following parameters were used to simulate D: K = 5, α0 = 1, ε = 0.2, G = 1. The methods were run without pre-processing (NA), after removal of confounding probes by linear regression (lm), after removal of confounding probes and filtering for the most variable probes (lm + var), and after removal of confounding probes and filtering of probes expected to biologically vary in methylation levels across constitutive cell types (lm + infloci)

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BMC Bioinformatics

ISSN: 1471-2105

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