Fig. 8

Examples of probes exhibiting obvious batch-effect. In some instances, probes had clear batch-effects which were corrected by application of Harman or ComBat. The panel layout is consistent with that in Fig. 7, with four examples of batch-effect prone probes illustrated. After batch correction, the SD was typically reduced and the computed LVR was considerably less than 0. Typically, as is the case with cg01381374, the particular influence of these probes on the data was idiosyncratic to the dataset. In other instances, there was high technical variance in one dataset but not the other. In the case of cg22256960, the batch-effect is limited to the EPIC superbatch 2 data. The example of cg27298252 highlights that batch-effect can be found both across arrays and by the position in the array. In particular, the EPIC data illustrate clear positional bias. The cg04294190 probe demonstrates that both technical and biological factors can contribute to methylation clustering. In this case, the data are clustered both by gender and within the 450K data, by slide number