ArticleFrontiers in genetics2018
Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned.
Article in Frontiers in genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 3 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
64 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Sex differences in muscle protein expression and DNA methylation in response to exercise training.Biology of sex differences · 2023Pooled it
- Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI.GigaScience · 2022Pooled it
- An effective processing pipeline for harmonizing DNA methylation data from Illumina's 450K and EPIC platforms for epidemiological studies.BMC research notes · 2021Pooled it
- Trial
- Extracellular vesicles and epigenetic aging clocks in tissue aging: an exosome-focused conceptual framework with a focus on skin.The journals of gerontology. Series A, Biological sciences and medical sciences · 2026Review
- Meta-Merging the Transcriptomes of Gastric Tumors Redefines the Connections among Molecular and Clinical Subtypes.Asian Pacific journal of cancer prevention : APJCP · 2026Article
- DNA methylation and telomere length in 2-5 year olds with intrauterine preeclampsia exposure: a P4 sub-study.Clinical epigenetics · 2025Article
- DNA methylation and machine learning: challenges and perspective toward enhanced clinical diagnostics.Clinical epigenetics · 2025Review
- Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools.Life science alliance · 2025Article
- A comprehensive guide to genomeZhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences · 2025Review
- Placental epigenetic clocks derived from crowdsourcing: Implications for the study of accelerated aging in obstetrics.iScience · 2025Article
- Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools.bioRxiv : the preprint server for biology · 2025Article
- ComBat-met: adjusting batch effects in DNA methylation data.NAR genomics and bioinformatics · 2025Article
- 5G-exposed human skin cells do not respond with altered gene expression and methylation profiles.PNAS nexus · 2025Article
- Caregiver-child interaction and early childhood development among preschool children in rural China: the possible role of blood epigenome-wide DNA methylation.BMC genomics · 2025Article
- Breaking rules: the complex relationship between DNA methylation and X-chromosome inactivation in the human placenta.Biology of sex differences · 2025Article
- HarmonizR: blocking and singular feature data adjustment improve runtime efficiency and data preservation.BMC bioinformatics · 2025Article
- Epigenetic age acceleration and neurotrophin signaling pathways in cancer-related cognitive impairment: a longitudinal, prospective cohort study.Frontiers in aging · 2025Article
- The DNA methylation landscape across the TCR loci in patients with acute myeloid leukemia.International immunopharmacology · 2024Article
- Epigenome-wide association study of lung cancer among never smokers in two prospective cohorts in Shanghai, China.Thorax · 2024Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is well-known, but frequently overlooked, that low- and high-throughput molecular data may contain batch effects, i.e., systematic technical variation. Confounding of experimental batches with the variable(s) of interest is especially concerning, as a batch effect may then be interpreted as a biologically significant finding. An integral step toward reducing false discovery in molecular data analysis includes inspection for batch effects and accounting for this signal if present. In a 30-sample pilot Illumina Infinium HumanMethylation450 (450k array) experiment, we identified two sources of batch effects: row and chip. Here, we demonstrate two approaches taken to process the 450k data in which an R function,
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.