Positional effects revealed in Illumina methylation array and the impact on analysis.

ABSTRACT:

Aim

We aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method.

Materials & methods

Three HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods.

Results

We detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset. The pre- and postcorrection comparisons indicate the positional effects could alter the measured methylation values and downstream analysis results.

Conclusion

Positional effects exist in the

SUBMITTER: Jiao C 

PROVIDER: S-EPMC6021926 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature