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Probes were filtered based on detection values generated by BeadStudio©.
Genes were then filtered based on detection values generated by BeadStudio©.
Another three individuals were removed based on detection p-values (> 0.01 for > 1% of probes) and 3,027 of 27,578 probes were excluded based on detection values (p>0.01 for > 1% of the samples).
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To evaluate a worst-case scenario, and in light of high analytical limits of detection, we calculated cancer risks based on detected values and 10-year exposure duration.
Next, a wide range of analysis parameters can be adjusted, such as normalization method (SWAN, Functional, Quantile, Noob or Illumina), quality control filtering based on detection p values, failed sample threshold, Q-value cutoff for multiple testing as well as genomic regions for testing.
We have not applied any filter based on detection P values.
The probe sets were filtered based on detection p-values.
A/P call detection was performed based on detection P-value.
They developed two pooled filters for each probeset based on detection p-values.
Sample weights based on detection p-values across samples were used in the lmFit function from the Limma package to downweight samples with higher detection p-values.
The algorithm performed (1) probe quality filtering based on detection p value, (2) removal of probes on sex chromosomes, (3) color bias adjustment and (4) SQN on the methylation estimates (β values) using the "relation to CpG" to calculate the reference quantiles.
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