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Fig. 3 | Clinical Epigenetics

Fig. 3

From: Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO

Fig. 3

Average fluorescence intensities of probes targeting the X chromosome (x-axis) or targeting the Y chromosome (y-axis), each normalized versus the average fluorescence of autosomal probe intensities per sample. Dotted lines represent the Hodges-Lehmann estimators separating the male and female cluster centers. Samples that are discordant for sex relative to their metadata annotation are considered mislabeled and shown in red. Samples falling in the lower left or upper right quadrant are considered “unclear”. a All 8327 samples from all 80 datasets. b A single dataset (dataset E) with a spread in the female cluster indicating varying degrees of contamination with male DNA

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