bioconductor-illuminaio

name: bioconductor-illuminaiodescription: Tools for parsing Illumina's microarray output files, including IDAT.when_to_use: "Use when: Raw IDAT parsing: Reading raw binary Illumina IDAT files from expression or genotyping microarrays using readIDAT.; Metadata extraction: Extracting per-bead-type values (e.g., MeanBinData, NumBeadsBinData, DevBinData) directly from Illumina BeadChip platforms.; Custom pipeline building: Providing a mechanism for developers of downstream analysis packages to extract all possible information from ID. Not for: High-level analysis: For end-to-end normalization and differential expression analysis, use downstream packages because illuminaio is strictly designed for raw file parsing and leaves data retention choices to the user.; Affymetrix microarrays: For A"user-invocable: false

illuminaio

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 0.54.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: base64
• Install: BiocManager::install("illuminaio")

When to Use

• Raw IDAT parsing: Reading raw binary Illumina IDAT files from expression or genotyping microarrays using readIDAT.
• Metadata extraction: Extracting per-bead-type values (e.g., MeanBinData, NumBeadsBinData, DevBinData) directly from Illumina BeadChip platforms.
• Custom pipeline building: Providing a mechanism for developers of downstream analysis packages to extract all possible information from IDAT files.

When NOT to Use

• High-level analysis: For end-to-end normalization and differential expression analysis, use downstream packages because illuminaio is strictly designed for raw file parsing and leaves data retention choices to the user.
• Affymetrix microarrays: For Affymetrix microarray data, use affy or oligo instead because illuminaio is exclusively built for Illumina BeadArray platforms.

Data Requirements

• Input format: Raw Illumina .idat files (e.g., _Grn.idat).
• Optional files: GenomeStudio output files (e.g., tab-separated text files) for comparison and validation.

Key Parameters

• file: Path to the .idat file to be parsed by readIDAT.

Best Practices

• Pass the file path directly to readIDAT; the function will automatically determine the IDAT format and call the appropriate internal reading routine.
• When comparing illuminaio output to GenomeStudio, remember to identify and remove internal control bead-types, as GenomeStudio excludes these automatically.
• Reorder the extracted bead-types numerically if comparing against GenomeStudio output, which sorts bead-types alphabetically.

Common Pitfalls

• Discrepancies with GenomeStudio: Small differences in summarized bead-intensity values when compared to GenomeStudio. Fix: Recognize that these are introduced by rounding performed by GenomeStudio that is not carried out by illuminaio.
• Mismatched bead-type counts: Having more bead-types in the illuminaio output than in GenomeStudio exports. Fix: Filter out the unannotated internal control bead-types that illuminaio extracts by default.

Alternatives

• minfi: High-level package for analyzing Illumina Infinium DNA methylation microarrays that uses illuminaio under the hood.
• beadarray: Specifically designed for Illumina BeadArray expression data, providing advanced normalization and QC beyond basic parsing.

Citations

• Mike L Smith, Keith A Baggerly, Henrik Bengtsson, Matthew E Ritchie, and Kasper D Hansen. illuminaio: An open source IDAT parsing tool for Illumina microarrays. F1000Research, 2:264, 2013.

References

• Homepage: https://bioconductor.org/packages/illuminaio
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/illuminaio/inst/doc/Description_of_Encrypted_IDAT_Format.pdf

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