RT Journal Article
SR Electronic
T1 Guidance on filtering DNA methylation microarray probes by detection p-values
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 245217
DO 10.1101/245217
A1 Jonathan A Heiss
A1 Allan C Just
YR 2018
UL http://biorxiv.org/content/early/2018/02/13/245217.abstract
AB DNA methylation microarrays are popular for epigenome-wide association studies, but spurious outlier values complicate downstream analysis. It was demonstrated previously that commonly used detection p-value cut-offs were insufficient and led to many calls on the Y-chromosome probes in females. We extend these observations by assessing 2,507 samples from 18 studies run on the 450K chip as well as outliers across technical replicates. We provide comprehensive guidance and software for filtering methylation microarrays as an essential step to reduce outliers.Disclosure of interest The authors report no conflict of interest.