ArticlePloS one2011
Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05151718 (Ependymomics), which is not on this map. Cited by 313 papers, 2 of them syntheses that pooled it.
What it found
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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.
Ependymomics: Multiomic Approach to Radioresistance of Ependymomas in Children and Adolescents
Who cites it
313 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Epigenome-wide association study of BMI in Black populations from InterGEN and GENOA.Obesity (Silver Spring, Md.) · 2023Pooled it
- Transcriptomic analysis of castration, chemo-resistant and metastatic prostate cancer elucidates complex genetic crosstalk leading to disease progression.Functional & integrative genomics · 2021Pooled it
- Effect of Intermittent Versus Continuous Low-Dose Aspirin on Nasal Epithelium Gene Expression in Current Smokers: A Randomized, Double-Blinded Trial.Cancer prevention research (Philadelphia, Pa.) · 2019Trial
- Best practices for using biological data in psychological research.Journal of mood and anxiety disorders · 2026Review
- CancerSubtyper: a deep learning framework for cancer subtyping through DNA methylation data.Epigenetics & chromatin · 2026Article
- Multi-Compartment Transcriptomics Identifies a Persistent Inflammatory Program and a Network-Derived Diagnostic Signature in Polycythemia Vera.International journal of molecular sciences · 2026Article
- Identification of mitochondria-related genes in calcific aortic valve disease by integrated analysis of single-cell and bulk transcriptomic atlases.Journal of physiology and biochemistry · 2026Article
- Defining PI3K Signaling as a Key Regulator of Molecular Heterogeneity and Inflammation in Glomerular Lupus Nephritis.Immune network · 2026Article
- Integrated multi-omics analysis reveals comprehensive metabolism-driven tumor heterogeneity and immune microenvironment in hepatocellular carcinomas.Scientific reports · 2026Article
- Meta-Merging the Transcriptomes of Gastric Tumors Redefines the Connections among Molecular and Clinical Subtypes.Asian Pacific journal of cancer prevention : APJCP · 2026Article
- Comprehensive assessment of unfolded protein response and its association with tumor progression in pan-cancer.iMetaOmics · 2026Article
- Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.Biology · 2026Article
- ReShuffle-MS: Region-Guided Data Augmentation Improves Artificial Intelligence-Based Resistance Prediction inMicroorganisms · 2026Article
- Tumor Microenvironment Characterization IdentifiesHuman mutation · 2026Article
- Development and comparison of evaluation metrics for batch correction reveals performance differences.Bioinformatics advances · 2026Article
- A novel batch effect correction framework for robust integration of high-variance data via a global-information virtual reference batch.Frontiers in microbiology · 2026Article
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- The significance of molecular heterogeneity in breast cancer batch correction and dataset integration.Breast cancer research : BCR · 2025Article
- Identification of diagnostic and prognostic phospholipid biomarkers in idiopathic pulmonary fibrosis via machine learning and in vivo validation.Human genomics · 2025Article
253 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
7 authors.
Funding
Abstract
The expression microarray is a frequently used approach to study gene expression on a genome-wide scale. However, the data produced by the thousands of microarray studies published annually are confounded by "batch effects," the systematic error introduced when samples are processed in multiple batches. Although batch effects can be reduced by careful experimental design, they cannot be eliminated unless the whole study is done in a single batch. A number of programs are now available to adjust microarray data for batch effects prior to analysis. We systematically evaluated six of these programs using multiple measures of precision, accuracy and overall performance. ComBat, an Empirical Bayes method, outperformed the other five programs by most metrics. We also showed that it is essential to standardize expression data at the probe level when testing for correlation of expression profiles, due to a sizeable probe effect in microarray data that can inflate the correlation among replicates and unrelated samples.
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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.