illumina-450k-epic-dataset-loading

illumina-450k-epic-dataset-loading

Summary

Load raw Illumina HumanMethylation450 (450K) and EPIC array data from .idat files or beta-valued matrices into R memory using ChAMP, validating that pre-filter probe counts match expected array manifests (485,512 for 450K; 867,531 for EPIC) before any quality-based filtering.

When to use

You have raw .idat files or a beta-valued matrix from an Illumina HumanMethylation450 or EPIC array experiment and need to import the full probe set into R for downstream quality control, normalization, and differential methylation analysis. This skill is the entry point for any ChAMP-based methylation array workflow.

When NOT to use

• Input data has already been filtered to a reduced probe set (e.g., cross-reactive probes removed, SNP-associated probes excluded) — the pre-filter probe count will not match expected values and validation will fail.
• Array type is not HumanMethylation450 or EPIC (e.g., mouse array, custom array) — use ChAMPdata's appropriate manifest instead.
• Data is already in a processed form (e.g., M-values, combat-corrected, ComBat-adjusted) rather than raw intensities or uncorrected beta-values — use appropriate post-hoc import methods instead of champ.load().

Inputs

• .idat files (paired Grn and Red channel files) from Illumina HumanMethylation450 or EPIC array
• beta-valued matrix with CpG rows and sample columns
• sample sheet or metadata file (CSV/TSV) mapping sample IDs to files

Outputs

• ChAMP data object (S4 object) containing raw methylation intensities or beta-values
• Pre-filter probe count (485,512 for 450K; 867,531 for EPIC)
• Sample metadata and QC flags attached to the object

How to apply

Use ChAMP's champ.load() or champ.import() function to ingest .idat files or matrix data, specifying the array type (450K or EPIC). The function automatically loads the corresponding probe manifest from ChAMPdata (which must be ≥2.23.1 for ChAMP ≥2.29.1). Before proceeding to filtering or normalization, inspect the returned object's probe count: it should equal exactly 485,512 for HumanMethylation450 arrays or 867,531 for EPIC arrays if no filtering has yet been applied. If counts deviate, verify that the correct array type was specified and that the .idat files or input matrix correspond to the declared platform. This validation step confirms successful data import and correct manifest loading before quality-based probe filtering.