biostudies-literatureRoss JPNational Heart Foundation of AustraliaScience and Industry Endowment FundDiabetes Australia58https://www.ebi.ac.uk/biostudies/studies/S-EPMC9055778biostudies-literatureUnknown14(1)<h4>Background</h4>Genomic technologies can be subject to significant batch-effects which are known to reduce experimental power and to potentially create false positive results. The Illumina Infinium Methylation BeadChip is a popular technology choice for epigenome-wide association studies (EWAS), but presently, little is known about the nature of batch-effects on these designs. Given the subtlety of biological phenotypes in many EWAS, control for batch-effects should be a consideration.<h4>Results</h4>Using the batch-effect removal approaches in the ComBat and Harman software, we examined two in-house datasets and compared results with three large publicly available datasets, (1214 HumanMethylation450 and 1094 MethylationEPIC BeadChips in total), and find that despite various forms of prClinical epigeneticsBatch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data.PMC9055778Future Leader FellowshipRP03-064van Dijk SMolloy PLOytam YSkilton MRRoss JPPhang MfalseBatch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data.<h4>Background</h4>Genomic technologies can be subject to significant batch-effects which are known to reduce experimental power and to potentially create false positive results. The Illumina Infinium Methylation BeadChip is a popular technology choice for epigenome-wide association studies (EWAS), but presently, little is known about the nature of batch-effects on these designs. Given the subtlety of biological phenotypes in many EWAS, control for batch-effects should be a consideration.<h4>Results</h4>Using the batch-effect removal approaches in the ComBat and Harman software, we examined two in-house datasets and compared results with three large publicly available datasets, (1214 HumanMethylation450 and 1094 MethylationEPIC BeadChips in total), and find that despite various forms of pr2022-01-01T00:00:00Z2022 Apr2026-05-31T01:08:36.397Z2025-04-03T22:51:13.196ZS-EPMC90557783548831510.1186/s13148-022-01277-9