The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Biometry: The Principles and Practice of Statistics in Biological Research
Sokal, R. R., & Rohlf, F. J. (1969) · Cited by 20,963
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288
Bioconductor: open software development for computational biology and bioinformatics
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,172
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
Irizarry, R. A. (2003) · Biostatistics · doi:10.1093/biostatistics/4.2.249 · Cited by 10,603
Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray
Schena, M., Shalon, D., Davis, R. W., & Brown, P. O. (1995) · Science · doi:10.1126/science.270.5235.467 · Cited by 9,609
Biometry. The Principles and Practice of Statistics in Biological Research
Fienberg, S. E., Sokal, R. R., Rohlf, F. J., Rohlf, F. J., & Sokal, R. R. (1970) · Biometrics · doi:10.2307/2529087 · Cited by 9,364
Adjusting batch effects in microarray expression data using empirical Bayes methods
Johnson, W. E., Li, C., & Rabinovic, A. (2007) · Biostatistics · doi:10.1093/biostatistics/kxj037 · Cited by 8,658
Hanley, J. A., & McNeil, B. J. (1983) · Radiology · doi:10.1148/radiology.148.3.6878708 · Cited by 7,016
Forming inferences about some intraclass correlation coefficients.
McGraw, K. O., & Wong, S. P. (1996) · Psychological Methods · doi:10.1037/1082-989x.1.1.30 · Cited by 6,903
Lamb, J., Crawford, E. D., Peck, D., Modell, J. W., Blat, I. C., Wrobel, M. J., Lerner, J., Brunet, J.-P., Subramanian, A., Ross, K. N., et al. (2006) · Science · doi:10.1126/science.1132939 · Cited by 5,257
Cited by
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
Chen, L., Ge, B., Casale, F. P., Vasquez, L., Kwan, T., Garrido-Martín, D., Watt, S., Yan, Y., Kundu, K., Ecker, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.026 · Cited by 679
Castel, D., Philippe, C., Calmon, R., Le Dret, L., Truffaux, N., Boddaert, N., Pagès, M., Taylor, K. R., Saulnier, P., Lacroix, L., et al. (2015) · Acta Neuropathologica · doi:10.1007/s00401-015-1478-0 · Cited by 664
A Guide to ComBat Harmonization of Imaging Biomarkers in Multicenter Studies
Orlhac, F., Eertink, J. J., Cottereau, A.-S., Zijlstra, J. M., Thieblemont, C., Meignan, M., Boellaard, R., & Buvat, I. (2022) · Journal of Nuclear Medicine · doi:10.2967/jnumed.121.262464 · Cited by 348
Batch effect removal methods for microarray gene expression data integration: a survey
Lazar, C., Meganck, S., Taminau, J., Steenhoff, D., Coletta, A., Molter, C., Weiss-Solis, D. Y., Duque, R., Bersini, H., & Nowe, A. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs037 · Cited by 333
Li, L., Ning, Z., Zhang, X., Mayne, J., Cheng, K., Stintzi, A., & Figeys, D. (2020) · Microbiome · doi:10.1186/s40168-020-00806-z · Cited by 328
Metadata
- Authors
- Chen, C., Grennan, K., Badner, J., Zhang, D., Gershon, E., Jin, L., & Liu, C.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-02-28
- Volume
- 6
- Issue
- 2
- Pages
- e17238
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W1986849266
- Cited by
- 542
- References
- 36
- FWCI
- 10.46
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods. https://app.cochat.ai/papers/10.1371/journal.pone.0017238
- The paper
- Chen, C., Grennan, K., Badner, J., Zhang, D., Gershon, E., Jin, L., & Liu, C. (2011). Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods. PLoS ONE. https://doi.org/10.1371/journal.pone.0017238
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
