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Fig. 2 | Clinical Epigenetics

Fig. 2

From: Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

Fig. 2

Multidimensional scaling plots of M values by batch and family. Multidimensional scaling plots for raw (a, b), stratified QN (c, d) and ComBat stratified QN (e, f) M values. For each plot, the 1000 most variable probes were selected. In a, c and e, numbers represent batches and are coloured accordingly, with clustering by batch clearly seen in a, to a lesser extent in c and removed in e. In b, d and f, numbers represent family groups and are coloured accordingly with the clearest clustering present in f after the batch effect has been removed. p values are from an ANOVA test for significance of batch (a, c and e) or family (b, d and f) on the first principal component from a PCA on the beta values

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