| name | bioconductor-illuminaio |
| description | 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
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