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minfi::getQC - badsamplecutoff 10.5

Hello,

I just started working on analyzing methylation EPIC array data using minfi. Data is generated on EPICv2 array and I'm using updated EPICv2 annotation (rgset@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38") Using the getQC and plotQC function. I noticed that all of samples are below 10.5 cut-off (lowest value is 9.1 and highest value is 10.48). Beta values density plot looks normal and detection p-value also looks normal. I'm confused on how should I interpret this data?

Thanks

getqc minfi methylation epicv2
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updated by Papyrus Papyrus • written by June • June

I've recently also analyzed EPICv2 and have noticed that the log2 median intensities (and particularly the "uMed" channel), for an otherwise good QC cohort, were lower than what I had seen in the past for EPICv1 in general. But my N for this observation was N = 1 EPICv2 cohort...

In my opinion if in your plotQC scatter plot your samples cluster together, and if the minfi::qcReport control probes look OK, this is more of a "general batch" thing and would proceed (only filtering out outliers further away from the cluster of points) but it would be nice to get feedback from more people analyzing EPICv2 to see if it's typical to get less absolute signal intensities.

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written by Papyrus Papyrus

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