Internal controls. Examples of sample-independent (A) and sample-dependent (B) plots generated by the HumMeth27QCReport package. a. Hybridization control, to check synthetic targets at low, medium, and high concentration level. Low percentage for each level is an indication of good performance; b. bisulfite control on green channel, to monitor the efficiency of genomic-DNA bisulfite conversion using the Infinium I assay design. Low percentage is an indication of good performance, whereas if the percentage is high we consider that the sample has lower performance. A detailed explanation of each plot is available at the HumMeth27QCReport homepage (http://biocore.crg.es/wiki/HumMeth27QCReport). JUR: Jurkat DNA; JUR MET: methylated Jurkat DNA; UNMET: unmethylated DNA; EZGOLD: EZ DNA Methylation-Gold Kit (Zymo Research, CA, USA); QIAGEN: EpiTect Bisulfite Kit (QiaGen); BIO1: biological replicate 1; BIO2: biological replicate 2; PD3 Amyg: example of sample of poor quality.