Infinium Mouse Methylation BeadChip FAQs

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  • Background subtraction is required when you compare data run on different types of scanners because of technical disparities. Background subtraction has a much smaller effect when you scan chips on the same scanner, and might not be necessary. Analyze a subset of data with and without subtraction, and choose the subset of data you prefer based on your results.

    What you are seeing are histograms of the beta values in bins of 0.02 steps and categorized by Infinium design type. The difference in beta value ranges between the Infinium I and Infinium II assay design types cause the double peaks. In general, the beta peaks at the extremes of Infinium I probes tend to be further out than the beta peaks for Infinium II.

    The beta beak differences do not affect the final analysis of the project. Individual CpG assays are not intended to be compared directly with other CpG assays, as each probe (or probe set for Infinium I designs) has different binding characteristics and behaves differently than any other probe or probe set. Rather, each assay is compared between two samples or sample groups (ie, in determining a relative rather than an absolute methylation value). For the Infinium HumanMethylation450K, Infinium Mouse Methylation, and Infinium MethylationEPIC array, we expect technical replicates to show > 98% correlation, and often observe > 99% correlation.

    SNPs were included on the BeadChip so investigators could generate a DNA fingerprint of their samples as an added level of quality control. Specifically, for the Mouse Methylation BeadChip, SNP probes are included to help identify the strain origin of the DNA being analyzed. Please find further information in the Infinium HD Methylation Assay Protocol Guide. SNP assays on the BeadChip are not mentioned in the assay guide and only briefly described in the GenomeStudio Methylation Module.

    The GenomeStudio Methylation Module extracts beta values and provides clustering and normalization for Infinium Mouse Methylation BeadChip data.

    Notably, there are many freeware applications in Bioconductor, such as chAMP, RnBeads, and SeSAMe, which provide enhanced normalization and visualization options. Illumina does not support these freeware solutions directly.