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array-preprocessing

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Turns raw Illumina Infinium methylation BeadChip IDATs (450K, EPIC, EPICv2) into a defensible beta/M matrix with sesame (openSesame/SigDF) or minfi (RGChannelSet -> MethylSet -> GenomicRatioSet). Covers Type I vs Type II probe chemistry and why raw Type II beta is compressed, the signal-to-beta math (beta = M/(M+U+100)) and M-value logit, detection-p / pOOBAH masking including the out-of-band deletion-artifact catch, dye-bias correction, and the normalization decision (noob, funnorm, quantile, SWAN, BMIQ, dasen, sesame QCDPB). Use when reading IDATs, choosing a normalization for a 450K/EPIC/EPICv2 cohort, deciding beta vs M, masking failed probes, or producing the corrected matrix before testing. For probe/sample filtering, EPICv2 replicate collapse, and sample-identity QC see array-qc-filtering; for native long-read 5mC see long-read-sequencing/nanopore-methylation (a different platform).

When to use

• reading IDATs
• choosing a normalization for a 450K/EPIC/EPICv2 cohort
• deciding beta vs M
• masking failed probes
• producing the corrected matrix before testing
• Type I vs Type II probe chemistry correction
• dye-bias correction
• detection-p / pOOBAH masking

When not to use

• probe/sample filtering
• EPICv2 replicate collapse
• sample-identity QC
• native long-read 5mC
• bisulfite-sequencing (Bismark/WGBS/RRBS)
• per-CpG testing
• region calling

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