Add docs on the Illumina refinery #154
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wvauclain
approved these changes
Aug 9, 2021
dvenprasad
approved these changes
Aug 9, 2021
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| We infer the Illumina BeadArray platform that a sample is likely to be run on by comparing the probe identifiers in the unprocessed file to probes for each of the Illumina expression arrays for a given organism. | ||
| We again use the Illumina Bioconductor annotation packages for this step. | ||
| For instance, the overlap between the probe identifiers in a human sample and the probe identifiers in each human platform (<a href = "https://www.bioconductor.org/packages/release/data/annotation/html/illuminaHumanv1.db.html" target = "blank">`v1`</a>, <a href = "https://www.bioconductor.org/packages/release/data/annotation/html/illuminaHumanv2.db.html" target = "blank">`v2`</a>, <a href = "https://www.bioconductor.org/packages/release/data/annotation/html/illuminaHumanv3.db.html" target = "blank">`v3`</a>, and <a href = "https://www.bioconductor.org/packages/release/data/annotation/html/illuminaHumanv4.db.html" target = "blank">`v4`</a>) is calculated. | ||
| The platform with the highest overlap (provided it is >75%) is inferred to be the true platform. | ||
| Some analyses around this platform detection procedure can be found in <a href = "https://github.com/jaclyn-taroni/beadarray-platform-detection" target = "blank">this repository</a>. | ||
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| ##### Handling Illumina probes that map to multiple Ensembl gene identifiers |
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We're gonna be linking them here right?
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That was my plan, yes!
jashapiro
approved these changes
Aug 11, 2021
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Thanks all! |
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Closes #153.
This adds text covering the Illumina refinery in our documentation.
It is largely adapted from the Illumina refinery README with a little more info/rationale thrown in.
(Side note: Is the
If none of the associated gene IDs appear in any Brainarray platform, an NA is emittedpoint in that README now out of date? I thought so and didn't add it here.)I also made a couple tweaks that I thought would help contextualize the newly added section.
Notes for reviewers