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kemal 579009271e v2 methylation QC validated on minfiDataEPIC and against sesame (K-026)

beta r 0.99998 vs sesame 1.28.1 (max |dbeta| 0.011), detection calls 99.1% identical,
noob within 0.5% median; replicate r 0.997; all 21 control metrics pass. Spec deviations
recorded (5-field control lines, pOOBAH formula, minfi sheet keys). User guide section.

2026-09-29 00:41:54 +01:00

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v2 module validation — methylation control QC (`simurg methyl qc`)

Date: 2026-09-29. Development on the Raspberry Pi; oracle runs on AWS (c7g.xlarge, five short runs, ≈ $0.025). Spec: MET-001 … MET-018 (and QC-004/QC-006, QC-062).

Data

minfiDataEPIC (Bioconductor, Artistic-2.0): 3 EPIC v1 arrays of NA12878 (IDATs + minfi-style sample sheet).
Infinium MethylationEPIC v1.0 B5 manifest (CSV): 865 918 probes (142 158 Infinium I: 92 212 red, 49 946 green), 635 control beads. Read in 8.6 s on the Pi.

Delivered

simurg methyl qc, simurg methyl convert-manifest, simurg qc controls --array-type methylation, methylation datasets in simurg qc report; modules formats/methyl_manifest.py, signal/methyl.py, pipeline/methyl.py; the 21 methylation metrics in qc/controls.py. User guide: "Methylation arrays".

Results on minfiDataEPIC

Check	Result
Run time, 3 samples, 3 workers (Pi)	25 s (2.9 s signal processing per sample)
21 control metrics	all evaluable, all pass the `methylation_epic` profile (e.g. staining green 57, BS conversion I green 13, BS conversion II 5.3, specificity II 24)
Probes passing detection (p < 0.05, analytical CG + SNP probes)	90.9 %, 91.1 %, 91.3 %
β of the three NA12878 replicates	Pearson r 0.997 – 0.9974 between replicates; bimodal distribution
Sheet `Sample_Group` → PCA colours; outputs of MET-013	present; folder loads in `qc report`

Against the sesame oracle (sesame 1.28.1, same probe set via `probes.tsv`/`controls.tsv`)

scripts/v2/sesame_oracle.R + scripts/v2/methyl_oracle_compare.py, bead-count masking off on both sides (sesame's min_beads masks every Infinium II probe because their M address is NA), 865 918 probes per sample:

Quantity	Agreement (3 samples)
β values	Pearson r 0.99998; \|Δβ\| median 0.0009, 99th percentile 0.008, max 0.011
noob-corrected M/U signals	relative difference median 0.5 %, max 5 %
Detection calls at p < 0.05	99.0 – 99.1 % identical; passing fraction 91.0 – 91.4 % (simurg) vs 92.0 – 92.3 % (sesame)
Detection p-values	not identical (median \|Δp\| 0.0008)

The remaining difference is systematic (same size in all three samples) and is not the negative controls: sesame did not attach the supplied control table (negControls failed, so its background is out-of-band Infinium I signal only), and simurg without negative controls is not closer (noob difference 0.56 % instead of 0.53 %). The exact cause is open (K-026). For QC use — pass/fail per sample, detection rate, β for a PCA — the agreement is sufficient; simurg's methylation numerics are documented as its own [OURS] implementation of the published methods (MET-010), not as a bit-exact port.

Spec deviations (K-026)

MET-002: the vendor EPIC manifest has a 5th field (AVG) on some NEGATIVE control lines; ≥ 4 fields are accepted and the first four used. Fewer than 4 still gives E_METH_CONTROLS_FORMAT.
MET-010: the detection p-value follows sesame's pOOBAH (p = 1 − max(F(M), F(U)), each in its own channel) instead of the ambiguous "1 − ECDF(M + U)", so an open-source oracle exists.
MET-004: Sentrix_ID/Sentrix_Position (minfi/sesame sheets) accepted as a third key-column pair.

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v2 module validation — methylation control QC (simurg methyl qc)