PT  - JOURNAL ARTICLE
AU  - Jonathan A Heiss
AU  - Allan C Just
TI  - Guidance on filtering DNA methylation microarray probes by detection p-values
AID  - 10.1101/245217
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 245217
4099  - http://biorxiv.org/content/early/2018/02/13/245217.short
4100  - http://biorxiv.org/content/early/2018/02/13/245217.full
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.