Journal
BIOINFORMATICS
Volume 32, Issue 3, Pages 469-471Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btv577
Keywords
-
Categories
Funding
- NCI [R37 CA76404, P01 CA134294, R35 CA197449]
- NIEHS [R01 ES015172, R01 ES021733, K99 ES023450]
- Gerstner Family Career Development Award
Ask authors/readers for more resources
The development of the Infinium HumanMethylation450 BeadChip enables epigenome-wide association studies at a reduced cost. One observation of the 450K data is that many CpG sites the beadchip interrogates have very large measurement errors. Including these noisy CpGs will decrease the statistical power of detecting relevant associations due to multiple testing correction. We propose to use intra-class correlation coefficient (ICC), which characterizes the relative contribution of the biological variability to the total variability, to filter CpGs when technical replicates are available. We estimate the ICC based on a linear mixed effects model by pooling all the samples instead of using the technical replicates only. An ultra-fast algorithm has been developed to address the computational complexity and CpG filtering can be completed in minutes on a desktop computer for a 450K data set of over 1000 samples. Our method is very flexible and can accommodate any replicate design. Simulations and a real data application demonstrate that our whole-sample ICC method performs better than replicate-sample ICC or variance-based method.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available