ArticleFrontiers in systems biology2023
Batch Correction and Harmonization of -Omics Datasets with a Tunable Median Polish of Ratio.
Article in Frontiers in systems biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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
37 citing papers in PubMed.
- A microprotein atlas of the human frontal cortex in Alzheimer's disease.Nature aging · 2026Article
- Metabolic reprogramming in the enterocytes of neonatal piglets infected with porcine epidemic diarrhea virus: integrated omics and multi-batch analysis highlight alterations in lipid metabolism and potential therapeutic targets.Microbiology spectrum · 2026Article
- Radon-Induced Radiation Biomarkers: A Scoping Review from Exposure Dosimetry to Early Biological Effects on the Lung.International journal of molecular sciences · 2026Article
- Neurodegeneration risk variants promote lysosomal TMEM106B fibril accumulation.bioRxiv : the preprint server for biology · 2026Article
- Granulin loss and TMEM106B risk converge on lysosomal C-terminal fragment pathology in frontotemporal dementia.bioRxiv : the preprint server for biology · 2026Article
- Multi-platform integration of brain and CSF proteomes reveals biomarker panels for Alzheimer's disease.Briefings in bioinformatics · 2026Article
- CSF Proteomics and Machine Learning Reveal Distinct Stages Across the Alzheimer's Disease Continuum.medRxiv : the preprint server for health sciences · 2025Article
- Article
- Protein-level batch-effect correction enhances robustness in MS-based proteomics.Nature communications · 2025Article
- Cerebrospinal fluid proteomics for predictive assessment of Alzheimer's Disease risk.medRxiv : the preprint server for health sciences · 2025Article
- Multi-scale integration of human brain vascular and CSF proteomes reveals biomarkers of cerebral amyloid angiopathy linked to Alzheimer's disease risk.medRxiv : the preprint server for health sciences · 2025Article
- Brain wide engraftment of human monocytes induces neurodegeneration and cognitive dysfunction.Research square · 2025Article
- Plasma proteomic associations with Alzheimer's disease endophenotypes.Nature aging · 2025Article
- Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions.Acta pharmaceutica Sinica. B · 2025Review
- The evolution of analytical techniques for multiplex analysis of protein biomarkers.Expert review of proteomics · 2025Review
- Proteomic analysis of Down syndrome cerebrospinal fluid compared to late-onset and autosomal dominant Alzheimer´s disease.Nature communications · 2025Article
- Multiplex Proteomics of Lewy Body Dementia Reveals Cerebrospinal Fluid Biomarkers of Disease Pathology and Progression.bioRxiv : the preprint server for biology · 2025Article
- Network analysis of the cerebrospinal fluid proteome reveals shared and unique differences between sporadic and familial forms of amyotrophic lateral sclerosis.Molecular neurodegeneration · 2025Article
- Extensive modulation of the circulating blood proteome by hormonal contraceptive use across two population studies.Communications medicine · 2025Article
- Longitudinal multi-omics in alpha-synuclein Drosophila model discriminates disease- from age-associated pathologies in Parkinson's disease.NPJ Parkinson's disease · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Large scale -omics datasets can provide new insights into normal and disease-related biology when analyzed through a systems biology framework. However, technical artefacts present in most -omics datasets due to variations in sample preparation, batching, platform settings, personnel, and other experimental procedures prevent useful analyses of such data without prior adjustment for these technical factors. Here, we demonstrate a tunable median polish of ratio (TAMPOR) approach for batch effect correction and agglomeration of multiple, multi-batch, site-specific cohorts into a single analyte abundance data matrix that is suitable for systems biology analyses. We illustrate the utility and versatility of TAMPOR through four distinct use cases where the method has been applied to different proteomic datasets, some of which contain a specific defect that must be addressed prior to analysis. We compare quality control metrics and sources of variance before and after application of TAMPOR to show that TAMPOR is effective at removing batch effects and other unwanted sources of variance in -omics data. We also show how TAMPOR can be used to harmonize -omics datasets even when the data are acquired using different analytical approaches. TAMPOR is a powerful and flexible approach for cleaning and harmonization of -omics data prior to downstream systems biology analysis.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.