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When there average methylation difference in radmeth is zero from the C/(C+T) estimates of each case-control, radmeth adjust outputs lines like this:
chr1 10866 + CpG -1 -1 -1-1 3 3 25 25
This causes issues to filter significant CpGs. For example we often do (and the documentation suggests on page 16) that we filter significant FDR-corrected CpGs using
When there average methylation difference in radmeth is zero from the
C/(C+T)
estimates of each case-control, radmeth adjust outputs lines like this:This causes issues to filter significant CpGs. For example we often do (and the documentation suggests on page 16) that we filter significant FDR-corrected CpGs using
This does not filter these lines with zero average difference. Should the p-values for these lines be 1 instead?
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