HI Marc, here's my PR to update Methyprep's pOOBAH pval calculation to closer match SeSAMe. This change produces negligible differences in assessing percent of passing probes so most users will not notice the change. This is especially the case for those analysing larger arrays. However, future array designs with greater infinium I content might pose a risk that without this change SeSAMe and Methylprep will disagree to a greater extent.
Here's the code snippit in SeSAMe that I based these changes off of. From my testing this change increases agreement between the two packages.
HI Marc, here's my PR to update Methyprep's pOOBAH pval calculation to closer match SeSAMe. This change produces negligible differences in assessing percent of passing probes so most users will not notice the change. This is especially the case for those analysing larger arrays. However, future array designs with greater infinium I content might pose a risk that without this change SeSAMe and Methylprep will disagree to a greater extent.
Here's the code snippit in SeSAMe that I based these changes off of. From my testing this change increases agreement between the two packages.
https://github.com/zwdzwd/sesame/blob/master/R/detection.R#L114
Cheers! Mauro