ArticlePloS one2008
Randomization in laboratory procedure is key to obtaining reproducible microarray results.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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.
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Who cites it
17 citing papers in PubMed, 39 citations in OpenAlex.
- Machine learning model for predicting Major Depressive Disorder using RNA-Seq data: optimization of classification approach.Cognitive neurodynamics · 2022Article
- Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies.Bioinformatics (Oxford, England) · 2021Article
- Fimbriae reprogram host gene expression - Divergent effects of P and type 1 fimbriae.PLoS pathogens · 2019Article
- Machine learning applied to transcriptomic data to identify genes associated with feed efficiency in pigs.Genetics, selection, evolution : GSE · 2019Article
- Metabolic perturbations in classic galactosemia beyond the Leloir pathway: Insights from an untargeted metabolomic study.Journal of inherited metabolic disease · 2019Article
- Proper experimental design requires randomization/balancing of molecular ecology experiments.Ecology and evolution · 2018Article
- Low-level maternal exposure to nicotine associates with significant metabolic perturbations in second-trimester amniotic fluid.Environment international · 2017Article
- Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets.BMC bioinformatics · 2016Article
- Article
- A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis.Bioinformatics (Oxford, England) · 2013Article
- Integrating murine gene expression studies to understand obstructive lung disease due to chronic inhaled endotoxin.PloS one · 2013Article
- Effect of population heterogenization on the reproducibility of mouse behavior: a multi-laboratory study.PloS one · 2011Article
- Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database.BMC bioinformatics · 2010Article
- Article
- Host-microbe interaction systems biology: lifecycle transcriptomics and comparative genomics.Future microbiology · 2010Review
- A longitudinal study of gene expression in healthy individuals.BMC medical genomics · 2009Article
- Prenatal exposure to escitalopram and/or stress in rats produces limited effects on endocrine, behavioral, or gene expression measures in adult male rats.Neurotoxicology and teratologyArticle
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
The quality of gene expression microarray data has improved dramatically since the first arrays were introduced in the late 1990s. However, the reproducibility of data generated at multiple laboratory sites remains a matter of concern, especially for scientists who are attempting to combine and analyze data from public repositories. We have carried out a study in which a common set of RNA samples was assayed five times in four different laboratories using Affymetrix GeneChip arrays. We observed dramatic differences in the results across laboratories and identified batch effects in array processing as one of the primary causes for these differences. When batch processing of samples is confounded with experimental factors of interest it is not possible to separate their effects, and lists of differentially expressed genes may include many artifacts. This study demonstrates the substantial impact of sample processing on microarray analysis results and underscores the need for randomization in the laboratory as a means to avoid confounding of biological factors with procedural effects.
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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.